[gmx-users] Restart dynamics when trr files removed
CROUZY Serge 119222
serge.crouzy at cea.fr
Tue May 14 16:34:12 CEST 2019
Hello Jon and Justin
I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella simulations using pull code)
I did try the -cpi option and my calculation seems to have restarted correctly renaming the files dyn.part0003....
But just running
gmx mdrun -cpi -noappend
does not allow me to tell the number of additional steps I want in my dynamics - So right now it's running 46 more ns (the original mdp and tpr file) which is not reasonable because I have 100s of calculations to run - I want to be able to specify 5 ns more for instance
Usually I use gmx convert-tpr - extend 5000 which builds a new tpr with which I can restart with -cpi
And running without a checkpoint file, Justin is not what I want - I really need to restart my dynamics after 46 ns, just I don't want the trr files - (I've got all the other files all right) - There should be a trick to restart without writing to a trr file... Isn't there ?
Thanks again for your help
Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Département des Interfaces pour l'Energie, la Santé et l'Environnement
Institut de Recherche Interdisciplinaire de Grenoble
CEA Grenoble UMR CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K pièce 110
Tel (33) 438782963
Fax (33) 438785487
http://big.cea.fr/drf/big/english/CBM/GMCT
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Envoyé : lundi 13 mai 2019 15:23
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Objet : gromacs.org_gmx-users Digest, Vol 181, Issue 30
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Today's Topics:
1. Gromacs error while running energy minimization step
(Muneeswaran S)
2. Re: ligand in water (Bratin Kumar Das)
3. Re: water mediated Hbond (Bratin Kumar Das)
4. nmr distance restraints (Eiso AB)
5. Restart dynamics when trr files removed (CROUZY Serge 119222)
6. Re: Restart dynamics when trr files removed (John Whittaker)
----------------------------------------------------------------------
Message: 1
Date: Mon, 13 May 2019 17:36:36 +0530
From: Muneeswaran S <wmunees47 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Gromacs error while running energy minimization
step
Message-ID:
<CAN=_HbdRYFT2pPAwmbmBx7EUiGKYSYcdjfdrgEoJq2+e+RBmDQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
I got the following error while running the gromacs
*NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected for this run.Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this
node:
PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1-------------------------------------------------------Program:
gmx mdrun, version 2018.6Source file: src/gromacs/utility/filestream.cpp
(line 115)Function: gmx::internal::FileStreamImpl::FileStreamImpl(const
char*, const char*)MPI rank: 12 (out of 16)System I/O error:Failed to
compile NBNXN kernels for GPU #Quadro P620 Could not open file '/usr/share/gromacs/opencl/nbnxn_ocl_kernels.cl
<http://nbnxn_ocl_kernels.cl>' Reason: No such file or directory
(call to fopen() returned error code 2)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>*
------------------------------
Message: 2
Date: Mon, 13 May 2019 18:15:27 +0530
From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] ligand in water
Message-ID:
<CAM7TW5t_i0Ckx64h9fk0r1X_-+-jx1fUxrg5xgmPDUH+4g9ncg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi
The procedure you are following is not ok. Generate the co-ordinate file of ligand and the topology parameter file. Setup the box and add water to it. Lastly do energy minimisation.
On Thu 9 May, 2019, 2:33 PM RAHUL SURESH, <drrahulsuresh at gmail.com> wrote:
> Hi Users.
>
> I want to simulate ligand in the water box. I prepared a water
> molecule and started with pdb2gmx and then planned to follow protein-ligand tutorial.
> Unfortunately ended up with an error in gro file format. Have check
> every possibility but still couldn't find any solution.
> My initial pdb is water.pdb and the corresponding gro file is
> water.gro. I clubbed the ligand gro file and water gro file as
> complex.gro. I have uploaded the file here. can anyone help me with the format issues>?
>
> --
> *Regards,*
> *Rahul *
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------------------------------
Message: 3
Date: Mon, 13 May 2019 18:18:38 +0530
From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] water mediated Hbond
Message-ID:
<CAM7TW5u-KQ6tzvcawBo=VztGr1enPQj+38br5=poNFRO+GJ4mQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
You can make a ndx file containing the residue of interest and the SOL. In gmx h-bond command use the index file. It will give you water mediated hbond
On Tue 7 May, 2019, 12:40 PM , <spss4 at iacs.res.in> wrote:
> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule. What extra flag should I use in gmx hbond command? Is
> there any other option to capture the water mediated Hbonds? Please
> suggest something.
> Sunipa Sarkar
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------------------------------
Message: 4
Date: Mon, 13 May 2019 14:49:17 +0200
From: Eiso AB <eisoab at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] nmr distance restraints
Message-ID:
<CAD3n-aaNenMX7g7XqmRorhmLwE8S3p_cY6qeLoZ4y=KpvJgRLw at mail.gmail.com>
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Hi,
I've setup an mdrun with [ distance restraints ] but the restraints don't seem to have any effect on the simulation, so I'm wondering if there's anything i need to do to switch them on that I missed.
gmx disre or gmx nmr doesn't give any info about restraints.
and the .log file doesn't show any energy component for Distance Restraints, e.g.
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.
4.14550e+03 1.13252e+04 1.29502e+04 9.20032e+01 6.00131e+02
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
5.01723e+03 6.08476e+04 3.13964e+05 -2.12124e+06 5.15532e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-1.70714e+06 2.85181e+05 -1.42196e+06 -1.34064e+06 2.99828e+02
Pressure (bar) Constr. rmsd
1.15517e+02 4.10744e-06
I have defined restraints between protein, ligand and a few waters - all in different [molecules]
- so I used [ intemolecular_interactions ] followed by [ distance restraints ]
my topol.top ends like this :
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
lig 1
SOL 35926
NA 4
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type' low up1 up2 fac ; # source
465 564 1 0 1 0.2540 0.2540 0.4115 1 ; # 308 ile hd+ 216 val hg1+
2.54
465 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
465 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
466 564 1 0 1 0.2540 0.2540 0.4115 1 ; #
466 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
466 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
467 564 1 0 1 0.2540 0.2540 0.4115 1 ; #
467 565 1 0 1 0.2540 0.2540 0.4115 1 ; #
467 566 1 0 1 0.2540 0.2540 0.4115 1 ; #
[...snap...]
1607 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # 170 leu hd1# 411 lig h09
5.68
1608 5241 1 34 1 0.5680 0.5680 0.6384 1 ; #
1609 5241 1 34 1 0.5680 0.5680 0.6384 1 ; # [ ..snap ... ]
2720 5571 1 52 2 0.1900 0.1900 0.2900 1 ; # 217 asp od1 501 sol hw2
1.90
2720 5569 1 53 2 0.3000 0.3000 0.4000 1 ; # 217 asp od1 501 sol ow
3.00
disre is set to simple. From the mdout.mdp
[]$ grep disre mdout.mdp
; Distance restraints type: No, Simple or Ensemble
disre = Simple
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
gmx dump shows that the run topology has the distance restraints and looks ok to me
gmx dump -s md_0_10.tpr |grep -10 dis
[..snap..]
Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision) Reading file md_0_10.tpr, VERSION 2019-beta1 (single precision)
disre = Simple
disre-weighting = Conservative
disre-mixed = false
nstdisreout = 100
0 type=1038 (DISRES) 464 563
1 type=1038 (DISRES) 464 564
2 type=1038 (DISRES) 464 565
3 type=1038 (DISRES) 465 563
4 type=1038 (DISRES) 465 564
5 type=1038 (DISRES) 465 565
[..snap ...]
D.R.Viol. (nm):
nr: 0
[...snap...]
functype[1038]=DISRES, label= 0, type=1, low= 2.54000008e-01,
up1= 2.54000008e-01, up2= 4.11500007e-01, fac= 1.00000000e+00)
functype[1039]=DISRES, label= 1, type=1, low= 2.56999999e-01,
up1= 2.56999999e-01, up2= 4.12600011e-01, fac= 1.00000000e+00)
functype[1040]=DISRES, label= 2, type=1, low= 3.72999996e-01,
up1= 3.72999996e-01, up2= 4.80199993e-01, fac= 1.00000000e+00)
functype[1041]=DISRES, label= 3, type=1, low= 3.84000003e-01,
up1= 3.84000003e-01, up2= 4.88200009e-01, fac= 1.00000000e+00)
functype[1042]=DISRES, label= 4, type=1, low= 2.33999997e-01,
up1= 2.33999997e-01, up2= 4.04900014e-01, fac= 1.00000000e+00)
functype[1043]=DISRES, label= 5, type=1, low= 2.39999995e-01,
up1= 2.39999995e-01, up2= 4.06699985e-01, fac= 1.00000000e+00)
functype[1044]=DISRES, label= 6, type=1, low= 3.03000003e-01,
up1= 3.03000003e-01, up2= 4.35000002e-01, fac= 1.00000000e+00)
etc...
Any suggestions about what is wrong here would be appreciated Thanks,
Eiso
------------------------------
Message: 5
Date: Mon, 13 May 2019 12:20:48 +0000
From: CROUZY Serge 119222 <serge.crouzy at cea.fr>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Restart dynamics when trr files removed
Message-ID:
<47AD30A9288C1E49BCF6C0CBB2E5BBA654C28587 at EXDAG0-A1.intra.cea.fr>
Content-Type: text/plain; charset="iso-8859-1"
Dear Gromacs users
I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)...
But NO - I can't restart the simulation from 50 ns on without trr files - Whatever tricks I seem to have tried to fool the controls I hope someone can tell me how I can solve my problem - Even if it is recompiling the source to remove the flag checking that the trr file is absent
Thanks for your help !
Serge Crouzy PhD HDR
Groupe de Mod?lisation et Chimie Th?orique Laboratoire de Chimie et Biologie des M?taux D?partement des Interfaces pour l'Energie, la Sant? et l'Environnement Institut de Recherche Interdisciplinaire de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K pi?ce 110
Tel (33) 438782963
Fax (33) 438785487
http://big.cea.fr/drf/big/english/CBM/GMCT
------------------------------
Message: 6
Date: Mon, 13 May 2019 15:22:41 +0200
From: "John Whittaker" <johnwhittake at zedat.fu-berlin.de>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Restart dynamics when trr files removed
Message-ID:
<51954.160.45.109.178.1557753761.webmail at webmail.zedat.fu-berlin.de>
Content-Type: text/plain;charset=utf-8
Hi,
> But NO - I can't restart the simulation from 50 ns on without trr
> files
There should be a checkpoint file called (by default) state.cpt that was generated when your 50 ns simulation finished. You can use this file to continue your run from the final state of that simulation with:
gmx mdrun -cpi state.cpt
Your checkpoint file might be named something different than "state.cpt", but regardless, that procedure should do the trick.
Good luck,
John
------------------------------
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