[gmx-users] Use trjconv in parallel
Tsjerk Wassenaar
tsjerkw at gmail.com
Sat Jul 5 14:47:29 CEST 2014
Hi Stephane,
Depending on what you want to do, it may be possible to split your
trajectory into frames (e.g. on /dev/shm) and process those in parallel,
joining the results into a new trajectory. You can contact me if you want a
python script for splitting an XTC file into frames.
Cheers,
Tsjerk
On Wed, Jul 2, 2014 at 2:15 PM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
wrote:
> Thanks for your quick and also fast (;)) reply, Carsten.
>
> Stéphane
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 2 Jul 2014 10:55:45 +0000
> From: ABEL Stephane 175950 <Stephane.ABEL 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] Use trjconv in parallel,
> Message-ID:
> <3E39B768BB199548AB18F7289E7534AF1B24FD38 at EXDAG0-B0.intra.cea.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> in short : it is possible ? I use the gromacs v4.6.5.
>
> Thanks
>
> St?phane
>
> ------------------------------
>
> Message: 5
> Date: Wed, 2 Jul 2014 13:44:08 +0200
> From: Carsten Kutzner <ckutzne at gwdg.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Use trjconv in parallel,
> Message-ID: <39B862CE-6E52-4590-9C57-BA34864B2271 at gwdg.de>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> On 02 Jul 2014, at 12:55, ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
> wrote:
>
> > Hello,
> >
> > in short : it is possible ? I use the gromacs v4.6.5.
> No.
>
> Carsten
> >
> > Thanks
> >
> > St?phane
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
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> send a mail to gmx-users-request at gromacs.org.
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 02 Jul 2014 07:50:34 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] grompp does not find atomtype
> Message-ID: <53B3F20A.7060105 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/2/14, 4:40 AM, Dawid das wrote:
> > I have managed to deal with this problem in following way:
> >
> > In topology file some bonding parameters were actually missing but some
> > bonding parameters were not needed, e.g. U-B or dihedral parameters for
> > atoms which are not connected, that is they belong to different parts of
> my
> > new residue.
> > I found parameters for the missing ones and hashed (;) them out. Is it
> what
> > I can do? Like I say, theses bonding parameters that I hashed out were
> for
> > atom types which are not connected directly.
> >
> > Then I performed minimization with steepest descent and in output file I
> > got:
> >
> > 4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep= 426, Dmax= 2.5e-06 nm,
> > Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep= 427, Dmax=
> 1.2e-06
> > nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 1000
> >
> > Double precision normally gives you higher accuracy.
> > You might need to increase your constraint accuracy, or turn
> > off constraints alltogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 428 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy = -4.5465475e+05
> > Maximum force = 1.7057922e+04 on atom 1003
> > Norm of force = 1.1677969e+02
> >
> > But I continued with NVT MD simulation. This is my nvt-md.mdp file:
> >
> > title = NVT MD
> > integrator = md
> > constraints = all-bonds
> > dt = 0.001
> > nsteps = 20000
> > nstenergy = 100
> > nstlist = 10
> > nstxout = 1000
> > nstvout = 1000
> > nstfout = 0
> > nstlog = 100
> > nstxtcout = 1000
> > xtcprecision = 500
> > ns_type = grid
> > coulombtype = PME
> > rlist = 1.0
> > rcoulomb = 1.0
> > rvdw = 1.0
>
> These cutoffs are incorrect for using CHARMM force fields. See previous
> posts
> on proper settings.
>
> > tcoupl = nose-hoover
> > tc-grps = Protein SOL NA
> > tau_t = 0.1 0.1 0.1 ;(3 numbers -> because 3 tc-grps)
> > ref_t = 100 100 100 ;(3 numbers -> because 3 tc-grps)
>
> Coupling water and ions separately is not sensible.
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do
>
> > Pcoupl = No
> > gen_vel = yes
> > gen_temp = 100
> > gen_seed = 173529
> > energygrps = Protein SOL NA
> > constraint_algorithm = LINCS
> > pbc = xyz
> >
> > And in my NVT output I got error for LINCS:
> >
> > relative constraint deviation after LINCS:
> > rms 0.036755, max 1.509884 (between atoms 998 and 1000)
> > bonds that rotated more than 30 degrees:
> > atom 1 atom 2 angle previous, current, constraint length
> > 1001 1003 62.1 0.1410 0.2032 0.1410
> > 1001 1002 68.1 0.1240 0.1962 0.1240
> > 1000 1001 88.1 0.1460 0.3276 0.1460
> > 998 1000 90.0 0.1390 0.3489 0.1390
> > 986 1000 90.7 0.1400 0.2237 0.1400
> > 985 986 30.7 0.1300 0.1499 0.1300
> > Wrote pdb files with previous and current coordinates
> >
> >
> > These atoms are those for my new residue. For next step I get more
> > constraint deviation.
> > Now, is it possible that this is because of wrong parameters? Or maybe I
> > should minimize my system further?
> > Here are all the files:
> >
> > http://www.speedyshare.com/jjvgd/md-simul.tar.bz2
> >
>
> When sharing files, please only post what is actually necessary to
> reproduce the
> problem - a self-contained force field directory, coordinates, topology,
> .mdp,
> and index file if needed. A dump of dozens of files with no context gets
> burdensome to go through.
>
> Your minimized geometry is clearly junk. Just visualize the structure and
> you
> will see that your mCherry residue is completely distorted. The very large
> (10^4) force after EM should have been the first clue that something is
> very wrong.
>
> The problems almost certainly stem from the manipulations you've made to
> the
> angles and dihedrals. I don't understand why you've commented some of
> them out.
> For instance, the first angle that you've removed is atoms 977-978-992,
> which
> clearly should have an angle interaction because 977-978 and 978-992 are
> bonded.
> Simply removing "inconvenient" interactions (i.e. lacking parameters or
> whatever) leads to a total meltdown of the model.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 123, Issue 7
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--
Tsjerk A. Wassenaar, Ph.D.
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