Updating examples

adavtyan · May 3, 2016 · e211990 · e211990
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commit e211990
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diff --git a/examples/1CTA_Dimer_Binding/1cta.in b/examples/1CTA_Dimer_Binding/1cta.in
@@ -16,7 +16,7 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	peptide
+atom_style	awsemmd
 
 bond_style harmonic
 

diff --git a/examples/1R69_AMH-Go/1r69.in b/examples/1R69_AMH-Go/1r69.in
@@ -16,7 +16,7 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	peptide
+atom_style	awsemmd
 
 bond_style harmonic
 

diff --git a/examples/1R69_single_memory/extended.in b/examples/1R69_single_memory/extended.in
@@ -16,7 +16,7 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	peptide
+atom_style	awsemmd
 
 bond_style harmonic
 
@@ -49,7 +49,7 @@ fix 11 all langevin 350.0 500.0 1000 3456  #change 3456 to other RANDOM numbers
 
 fix		  2 alpha_carbons backbone beta_atoms oxygens fix_backbone_coeff.data extended.seq
 
-thermo		2000
+thermo		1000
 dump		1 all atom 2000 1_dump
 
 dump_modify	1 sort id

diff --git a/examples/1R69_single_memory/folding.in b/examples/1R69_single_memory/folding.in
@@ -16,14 +16,16 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	peptide
+atom_style	awsemmd
 
 bond_style harmonic
 
 pair_style vexcluded 2 3.5 3.5
 
-read_restart unfold.restart
-#read_data data.1r69
+# The original example used the read_restart 
+# The restart file has to be regenerated for the newest version of LAMMPS
+#read_restart unfold.restart
+read_data data.1r69
 
 pair_coeff * * 0.0
 pair_coeff 1 1 20.0 3.5 4.5

diff --git a/examples/1R69_single_memory/unfolding.in b/examples/1R69_single_memory/unfolding.in
@@ -16,7 +16,7 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	peptide
+atom_style	awsemmd
 
 bond_style harmonic
 

diff --git a/examples/1SRL_Go-Model/1srl.ca.xyz b/examples/1SRL_Go-Model/1srl.ca.xyz
@@ -0,0 +1,57 @@
+56
+15.308	14.18	-2.955
+13.365	10.96	-3.638
+11.955	8.304	-1.278
+12.337	4.503	-1.101
+8.698	3.386	-1.481
+9.689	-0.159	-0.446
+12.826	-1.976	0.751
+14.082	-3.493	-2.542
+15.681	-6.745	-1.322
+18.302	-6.999	-4.096
+20.139999	-10.348	-4.237
+23.450001	-9.487	-5.951
+26.087	-7.065	-4.619
+25.799	-5.071	-7.867
+22.674	-3.343	-6.505
+22.423	-2.435	-2.805
+19.118999	-3.195	-1.097
+17.813	-0.013	0.538
+14.688	0.475	2.649
+11.65	2.762	2.965
+12.012	5.938	5.057
+15.719	6.262	4.188
+16.908001	9.273	2.157
+18.569	8.522	-1.201
+20.018999	10.839	-3.873
+18.903	9.663	-7.336
+21.764999	9.577	-9.866
+20.539	8.94	-13.423
+17.677999	7.228	-15.305
+14.692	9.612	-15.232
+12.225	7.211	-16.891001
+10.696	4.373	-14.843
+13.137	1.438	-14.598
+16.122	0.99	-12.243
+17.858999	4.268	-11.432
+21.014	4.235	-9.29
+20.833	6.244	-6.051
+23.716	7.111	-3.699
+23.222	7.134	0.092
+24.539	10.272	1.83
+25.201	8.354	5.068
+28.086	6.035	4.117
+28.283001	6.838	0.388
+27.500999	3.458	-1.212
+25.961	3.02	-4.681
+22.83	0.862	-5.027
+20.312	0.557	-7.884
+16.933001	1.473	-6.344
+13.969	0.178	-8.373
+11.809	2.989	-9.801
+8.67	1.183	-8.595
+10.322	1.101	-5.155
+11.125	4.842	-5.177
+9.2	8.091	-5.691
+10.073	11.79	-6.056
+9.02	12.876	-2.544
diff --git a/examples/1SRL_Go-Model/1srl.in b/examples/1SRL_Go-Model/1srl.in
@@ -2,11 +2,10 @@
 
 units real
 
-timestep 30
+timestep 20
 
 dimension	3
 
-#boundary s s s
 boundary p p p
 
 neighbor	5 bin
@@ -16,24 +15,34 @@ atom_modify sort 0 0.0
 
 special_bonds fene
 
-atom_style	bond
+atom_style	awsemmd
 
-read_restart unfolded.1srl.restart
-#read_data data.1srl
+#read_restart start.restart
+read_data data.1srl
 
 velocity        all create 300.0 23492
 
 group           alpha_carbons id 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56
 
-fix		  1 all nvt 300.0 300.0 50.0
+#compute         1 alpha_carbons qonuchic qonuchic.dat shadow 1srl_cmap.shadow 1.2
+compute         1 alpha_carbons qonuchic cutoff 8.0 1srl.ca.xyz 1.2
+
+variable q equal c_1
+
+fix		  1 all nvt temp 300.0 300.0 1000.0
 fix		  2 alpha_carbons gomodel fix_gomodel_coeff.data
-#fix		  3 alpha_carbons qbias fix_qbias_coeff.data
+#fix		  3 alpha_carbons momentum 10000 angular
+#fix		  4 alpha_carbons qbias fix_qbias_coeff.data
+fix               q all print 1000 "$q" file q.txt screen no &
+
+thermo		1000
+dump		1 all atom 1000 dump.lammpstrj
+restart         100000 restart.1srl
+
+dump_modify	1 sort id
 
-thermo		100
-dump		1 all atom 100 dump.lammpstrj
-restart         1000 restart.1srl
+thermo_style custom step temp pe etotal v_q press vol
 
-dump_modify     1 sort id
+reset_timestep  0
 
-reset_timestep	0
-run		10000
+run             1000000
diff --git a/examples/1SRL_Go-Model/data.1srl b/examples/1SRL_Go-Model/data.1srl
@@ -12,70 +12,70 @@ LAMMPS protain data file
            0  dihedral types
            0  improper types
 
--50.0	50.0	xlo xhi
--50.0	50.0	ylo yhi
--50.0	50.0	zlo zhi
+-100.0	100.0	xlo xhi
+-100.0	100.0	ylo yhi
+-100.0	100.0	zlo zhi
 
 Masses
 
            1	118.0
 
 Atoms
 
-           1	1	1	1.438	0.0	0.0
-           2	2	1	2.59378761	-3.45591638	-1.18385387
-           3	3	1	6.01734262	-4.69760916	-2.37472881
-           4	4	1	7.22169708	-6.59011248	-5.48096037
-           5	5	1	8.87240897	-9.62665998	-3.82710351
-           6	6	1	10.34008593	-10.51939563	-7.25196269
-           7	7	1	10.33682254	-8.96996002	-10.75623888
-           8	8	1	7.60390973	-11.01220248	-12.50012716
-           9	9	1	9.0184166	-10.84110498	-16.05689661
-          10	10	1	5.64163557	-11.12046167	-17.84575735
-          11	11	1	6.02951136	-11.618081	-21.62499542
-          12	12	1	2.75113842	-10.33605182	-23.13806681
-          13	13	1	1.43880744	-6.7506337	-22.8166989
-          14	14	1	-1.814449	-8.1478655	-21.35219256
-          15	15	1	-0.04960208	-8.52674121	-17.97247637
-          16	16	1	2.55701835	-5.93807855	-16.88386783
-          17	17	1	5.73531788	-7.32945919	-15.25808033
-          18	18	1	6.23146011	-5.52296347	-11.91575642
-          19	19	1	9.11219362	-5.95328085	-9.42639619
-          20	20	1	9.76293596	-6.48860109	-5.68865895
-          21	21	1	10.06003154	-3.35124818	-3.50933246
-          22	22	1	7.76115944	-1.28099071	-5.76984879
-          23	23	1	4.49105457	0.05513004	-4.28596588
-          24	24	1	1.28943537	-1.0618057	-6.07000682
-          25	25	1	-2.40905998	-0.34393402	-5.37250745
-          26	26	1	-4.43066204	-3.5652527	-5.83828005
-          27	27	1	-7.63867995	-2.89428424	-7.82300559
-          28	28	1	-10.03221839	-5.88552976	-7.88732448
-          29	29	1	-10.00176944	-9.7123348	-7.69931101
-          30	30	1	-9.49898049	-10.58875462	-4.00339372
-          31	31	1	-8.98247013	-14.35430231	-4.48772895
-          32	32	1	-5.59744015	-15.55081093	-5.82588147
-          33	33	1	-5.48977097	-15.26297382	-9.64507905
-          34	34	1	-4.84845908	-12.22509683	-11.89023727
-          35	35	1	-6.16220239	-8.87427773	-10.57615855
-          36	36	1	-5.64729716	-5.7919218	-12.7930635
-          37	37	1	-3.70081253	-2.93616976	-11.13879906
-          38	38	1	-3.20490931	0.61984617	-12.47653734
-          39	39	1	0.08660689	2.50304269	-11.9286277
-          40	40	1	-0.4382156	6.09202441	-10.69392751
-          41	41	1	2.86206084	7.28115287	-12.23498621
-          42	42	1	2.20173143	6.99518589	-15.9983492
-          43	43	1	-1.22863947	5.28981602	-15.92776532
-          44	44	1	-0.64755894	2.02610525	-17.84902802
-          45	45	1	-2.81001386	-1.10186228	-17.37964455
-          46	46	1	-1.08582901	-4.44336148	-16.64324611
-          47	47	1	-2.49008046	-7.70775881	-15.2105909
-          48	48	1	-0.33792376	-8.34461819	-12.10521738
-          49	49	1	-0.55168843	-11.97127215	-10.8876794
-          50	50	1	-2.0201208	-12.01430059	-7.34895535
-          51	51	1	0.71031191	-14.45971301	-6.23297673
-          52	52	1	3.2463024	-12.00201586	-7.71931111
-          53	53	1	1.75286563	-8.92723173	-5.98839743
-          54	54	1	0.82272941	-7.90487274	-2.41483594
-          55	55	1	-0.83790275	-4.90223175	-0.70979609
-          56	56	1	2.45796671	-3.5074861	0.65864902
+           1	1	1	1	0.0	15.30799961	14.18000031	-2.95499992
+           2	1	2	1	0.0	13.36499977	10.96000004	-3.63800001
+           3	1	3	1	0.0	11.95499992	8.3039999	-1.278
+           4	1	4	1	0.0	12.33699989	4.50299978	-1.10099995
+           5	1	5	1	0.0	8.69799995	3.38599992	-1.48099995
+           6	1	6	1	0.0	9.68900013	-0.15899999	-0.44600001
+           7	1	7	1	0.0	12.82600021	-1.97599995	0.75099999
+           8	1	8	1	0.0	14.08199978	-3.49300003	-2.54200006
+           9	1	9	1	0.0	15.68099976	-6.74499989	-1.32200003
+          10	1	10	1	0.0	18.30200005	-6.99900007	-4.09600019
+          11	1	11	1	0.0	20.13999939	-10.34799957	-4.23699999
+          12	1	12	1	0.0	23.45000076	-9.48700047	-5.95100021
+          13	1	13	1	0.0	26.08699989	-7.06500006	-4.61899996
+          14	1	14	1	0.0	25.79899979	-5.0710001	-7.8670001
+          15	1	15	1	0.0	22.67399979	-3.34299994	-6.50500011
+          16	1	16	1	0.0	22.42300034	-2.43499994	-2.80500007
+          17	1	17	1	0.0	19.11899948	-3.19499993	-1.097
+          18	1	18	1	0.0	17.81299973	-0.013	0.53799999
+          19	1	19	1	0.0	14.68799973	0.47499999	2.64899993
+          20	1	20	1	0.0	11.64999962	2.76200008	2.96499991
+          21	1	21	1	0.0	12.01200008	5.9380002	5.05700016
+          22	1	22	1	0.0	15.71899986	6.26200008	4.1880002
+          23	1	23	1	0.0	16.90800095	9.27299976	2.15700006
+          24	1	24	1	0.0	18.56900024	8.52200031	-1.20099998
+          25	1	25	1	0.0	20.0189991	10.83899975	-3.87299991
+          26	1	26	1	0.0	18.90299988	9.66300011	-7.33599997
+          27	1	27	1	0.0	21.76499939	9.57699966	-9.86600018
+          28	1	28	1	0.0	20.53899956	8.93999958	-13.42300034
+          29	1	29	1	0.0	17.6779995	7.22800016	-15.30500031
+          30	1	30	1	0.0	14.69200039	9.61200047	-15.23200035
+          31	1	31	1	0.0	12.22500038	7.21099997	-16.89100075
+          32	1	32	1	0.0	10.6960001	4.37300014	-14.84300041
+          33	1	33	1	0.0	13.13700008	1.43799996	-14.59799957
+          34	1	34	1	0.0	16.12199974	0.99000001	-12.24300003
+          35	1	35	1	0.0	17.85899925	4.26800013	-11.43200016
+          36	1	36	1	0.0	21.01399994	4.23500013	-9.28999996
+          37	1	37	1	0.0	20.83300018	6.24399996	-6.05100012
+          38	1	38	1	0.0	23.7159996	7.11100006	-3.69899988
+          39	1	39	1	0.0	23.22200012	7.13399982	0.092
+          40	1	40	1	0.0	24.53899956	10.27200031	1.83000004
+          41	1	41	1	0.0	25.20100021	8.35400009	5.06799984
+          42	1	42	1	0.0	28.08600044	6.03499985	4.1170001
+          43	1	43	1	0.0	28.28300095	6.83799982	0.38800001
+          44	1	44	1	0.0	27.50099945	3.45799994	-1.21200001
+          45	1	45	1	0.0	25.96100044	3.01999998	-4.68100023
+          46	1	46	1	0.0	22.82999992	0.86199999	-5.02699995
+          47	1	47	1	0.0	20.31200027	0.55699998	-7.88399982
+          48	1	48	1	0.0	16.93300056	1.47300005	-6.34399986
+          49	1	49	1	0.0	13.96899986	0.178	-8.37300014
+          50	1	50	1	0.0	11.80900002	2.98900008	-9.80099964
+          51	1	51	1	0.0	8.67000008	1.18299997	-8.59500027
+          52	1	52	1	0.0	10.32199955	1.10099995	-5.15500021
+          53	1	53	1	0.0	11.125	4.84200001	-5.17700005
+          54	1	54	1	0.0	9.19999981	8.0909996	-5.69099998
+          55	1	55	1	0.0	10.07299995	11.78999996	-6.05600023
+          56	1	56	1	0.0	9.02000046	12.8760004	-2.54399991