[gmx-users] umbrella sampling, LINCS WARNING
Justin Lemkul
jalemkul at vt.edu
Thu Jan 4 14:44:51 CET 2018
On 1/4/18 2:48 AM, rose rahmani wrote:
> Hello;
>
> I'm doing umbrella sampling, protein is getting closer to ZnS, but i get
> some step files and run crashed just 107sec to end. Would it be because of
> protein got very close to ZnS? Would you please help me?
A COM distance of 0.3 nm is going to place atoms well within the steep
LJ repulsive regime, so naturally forces are going to build up. Watch
the trajectory and see what's happening.
-Justin
> With regards
>
>
> ---------------------
> this is pullf.xvg
>
> 0.0000 -0.000579208
> 0.0020 2.45011
> 0.0040 4.89696
> 0.0060 7.35804
> 0.0080 9.82449
> 0.0100 12.2863
> 0.0120 14.7352
> 0.0140 17.1628
> 0.0160 19.5634
>
> .
> .
> .
> 1956.0480 -100532
> 1956.0500 -100532
> 1956.0520 -100531
> 1956.0540 -100530
> 1956.0560 -100529
> 1956.0580 -100528
> 1956.0600 -100527
> 1956.0620 -100526
> -----------
> this is pullx.xvg
>
> 0.0000 4.287 1.73577
> 0.1000 4.287 1.72023
> 0.2000 4.287 1.73131
> 0.3000 4.287 1.75326
> 0.4000 4.287 1.77348
> 0.5000 4.287 1.76939
> 0.6000 4.287 1.75636
> 0.7000 4.287 1.73677
> 0.8000 4.287 1.71755
> 0.9000 4.287 1.70901
> 1.0000 4.287 1.72336
>
> .
> .
> .
>
> 1953.2000 4.287 0.324765
> 1953.3000 4.287 0.323972
> 1953.4000 4.287 0.326929
> 1953.5000 4.287 0.323881
> 1953.6000 4.287 0.323358
> 1953.7000 4.287 0.325145
> 1953.8000 4.287 0.32516
> 1953.9000 4.287 0.324791
> 1954.0000 4.287 0.325144
> 1954.1000 4.287 0.324902
> 1954.2000 4.287 0.324985
> 1954.3000 4.287 0.324877
> 1954.4000 4.287 0.323429
> 1954.5000 4.287 0.32637
> 1954.6000 4.287 0.324941
> 1954.7000 4.
>
> -----------------------------------
> this is md_pull.mdp;
>
> integrator = md
> dt = 0.002
> nsteps = 1000000
> nstxout = 5000
> nstvout = 5000
> nstfout = 500
> nstlog = 500
> nstenergy = 1000
> nstxtcout = 1000
> nstlist = 10
> rlist = 1.5
> coulombtype = pme
> rcoulomb = 1.5
> vdwtype = Switch
> rvdw_switch = 1.0
> rvdw = 1.2
> pcoupl = no
> gen_vel = no
> constraints = h-bonds
> ns_type = grid
> pbc = xy
> freezegrps = WAL ZnS
> freezedim = Y Y Y Y Y Y
> energygrp-excl = WAL WAL ZnS ZnS
> energygrps = SOL WAL ZnS Protein NA CL
> nwall = 2
> wall-atomtype = C C
> wall-type = 9-3
> wall-density = 150 150
> wall-ewald-zfac = 3
> ewald-geometry = 3dc
> fourierspacing = 0.12
> tcoupl = v-rescale
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
>
> ; Pull code
> pull = umbrella
> pull_ngroups = 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry = direction
> pull_vec1 = 0 0 1
> pull_dim = N N Y
> pull_rate1 = -0.011 ; 1 nm per ns
> pull_k1 = 5000
> pull_start = yes
> pull_nstxout = 50
>
> --------------------------
> This is pull.job
>
>
> Step 978195, time 1956.39 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000004, max 0.000010 (between atoms 782 and 780)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 770 769 61.4 0.1090 0.1090 0.1090
> 779 778 42.0 0.1010 0.1010 0.1010
>
> Step 978197, time 1956.39 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.429802, max 1.468930 (between atoms 783 and 780)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 773 771 90.0 0.1112 0.1202 0.1090
> 770 769 32.8 0.1090 0.1090 0.1090
> 779 778 90.0 0.1010 0.1232 0.1010
> 783 780 90.0 0.1090 0.2691 0.1090
> Wrote pdb files with previous and current coordinates
>
> Step 978198, time 1956.4 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 2.212948, max 5.521000 (between atoms 773 and 771)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 773 771 90.0 0.1202 0.7108 0.1090
> 772 771 47.8 0.1105 0.1031 0.1090
> 770 769 90.0 0.1090 0.1142 0.1090
> 779 778 90.0 0.1232 0.6381 0.1010
> 783 780 57.8 0.2691 0.1086 0.1090
> Wrote pdb files with previous and current coordinates
>
> Step 978199, time 1956.4 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.451943, max 1.210712 (between atoms 770 and 769)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 773 771 90.0 0.7108 0.1628 0.1090
> 772 771 36.8 0.1031 0.1131 0.1090
> 770 769 90.0 0.1142 0.2410 0.1090
> 779 778 56.6 0.6381 0.1010 0.1010
> 783 780 90.0 0.1086 0.2027 0.1090
> Wrote pdb files with previous and current coordinates
> vol 0.70 imb F 27%
> Step 978200, time 1956.4 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 3.021436, max 9.508962 (between atoms 769 and 770)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 769 770 90.0 0.2410 1.1455 0.1090
> 773 771 90.0 0.1628 0.6838 0.1090
> 772 771 90.0 0.1131 0.6719 0.1090
> 779 778 90.0 0.1010 0.2717 0.1010
> 783 780 90.0 0.2027 0.1641 0.1090
> 782 780 90.0 0.1112 0.1303 0.1090
> 781 780 90.0 0.1097 0.2685 0.1090
>
> step 978200: Water molecule starting at atom 991 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> ^Mstep 978200, remaining runtime: 107 s
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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