[gmx-users] NVT problem (Justin Lemkul)
Tom
dnaafm at gmail.com
Sun Mar 16 00:27:19 CET 2014
Justin
Thanks for your quick response!
Yes, I used "periodic_molecules = yes"
It is correct to use this, right?
I just can not figuire out why single core can work but can not work
muli-cores.
Is it because i did not assign the charge groups on my surface atoms?
Thanks for the help!
Thom
On Sat, Mar 15, 2014 at 5:31 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: NVT problem (Andres Ortega Guerrero)
> 2. problem of running multiple cores (Tom)
> 3. Re: NVT problem (Justin Lemkul)
> 4. Re: problem of running multiple cores (Justin Lemkul)
> 5. Re: NVT problem (Andres Ortega Guerrero)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 15 Mar 2014 21:29:35 +0000
> From: Andres Ortega Guerrero <og_andres15 at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] NVT problem
> Message-ID: <BLU181-W692EF32A0EB84C519B28DE93730 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Justin,
>
> I have done a 1ns MD with DOX + water + CL ion , the topology didn?t
> present any problem,
>
> i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when i
> was trying to do my nvt.mdp
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.003859, max 0.176655 (between atoms 47397 and 47398)
> bonds that rotated more than 30 degrees:
>
> WARNING: Listed nonbonded interaction between particles 7156 and 7175
> at distance 3f which is larger than the table limit 3f nm.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> this are the warning that appear, so based on this, the main problem seems
> like to be my structure right?
> maybe, the DOX is misplaced or something like that, so should i prepare
> again the .gro files?
>
> Thanks in advance Justin,
>
> Andres Ortega
> Universidad del Valle (Colombia)
> Bionanoelectronics Research Group
>
> > Date: Sat, 15 Mar 2014 16:02:43 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] NVT problem
> >
> >
> >
> > On 3/15/14, 3:59 PM, Andres Ortega Guerrero wrote:
> > > Thank you Justin
> > >
> > > 1) Yes it can get a lower emtol
> > >
> > > 4)i?m using OPLS-AA ,FF
> > > 5) DOX is Doxorubicin,
> > >
> > > DOX.itp :
> > >
> > > 1) The structure was optimize with Gaussian and the charges was
> calculated to 1,
> > > 2) DOX.itp was generated by MKTOP, but i have to select 2 different
> atoms, and find the Diheradrals that was missing
> > >
> >
> > A simple simulation of DOX in water will indicate whether the topology
> is stable.
> >
> > The larger issue is using flexible water for EM and not minimizing again
> with
> > constraints. Inspect the energy-minimized geometry; I suspect you will
> find
> > some distorted waters. Given that NVT fails immediately, it suggests
> that there
> > is an unresolvable geometry problem, despite the apparent success of EM.
> >
> > -Justin
> >
> > >
> > > Thanks Justin
> > >
> > >> Date: Sat, 15 Mar 2014 15:41:11 -0400
> > >> From: jalemkul at vt.edu
> > >> To: gmx-users at gromacs.org
> > >> Subject: Re: [gmx-users] NVT problem
> > >>
> > >>
> > >>
> > >> On 3/15/14, 3:37 PM, Andres Ortega Guerrero wrote:
> > >>> Thank you Justin for Your Help, and advice, i have already the
> modification on the nvt.mdp that you suggest, but the problem is still
> there, my system has about 150.000 atoms , and for the energy minization i
> used DFLEXIBLE, and emtol was ajusted to 1000, i take a look to the
> steep0.pdb that gromacs produce, and there are atoms out of the box, but
> the DOX molecule is OK
> > >>>
> > >>> what would you suggest?
> > >>> - a emtol lower?
> > >>> - a water and dox md? ( maybe the DOX.itp can be the problem) ?
> > >>>
> > >>
> > >> Several ideas/questions:
> > >>
> > >> 1. Does energy minimization complete adequately? Can it proceed
> further (lower
> > >> emtol than 1000)?
> > >> 2. If you have used flexible water, you should re-minimize with
> > >> constraints/rigid water. It is common that a minimized system has
> badly
> > >> distorted the geometry of one or more water molecules.
> > >> 3. "Out of the box" is not an issue if you are using PBC, because no
> such thing
> > >> exists. If something has gone flying out of the rendered unit cell
> (i.e. large
> > >> coordinates), that suggests severe instability of the initial
> configuration and
> > >> would be a likely source of the problem.
> > >> 4. What force field are you using?
> > >> 5. What is the source of your DOX.itp parameters? What is DOX?
> > >>
> > >> -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
> > >>
> > >> ==================================================
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail to
> gmx-users-request at gromacs.org.
> > >
> > >
> >
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 15 Mar 2014 16:55:13 -0500
> From: Tom <dnaafm at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: [gmx-users] problem of running multiple cores
> Message-ID:
> <
> CAARYzz4hDFtnPnZYrbAM22s-B_9c_mxsZ4eH5WmukGmzdrS_ig at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gromacs Users
>
> I created a Silca surface with PBC bonding with the image atoms and
> assigned
> all the intramolecular potentials.
>
> It is strange that the generated *tpr can not be run with Multiple cores.
> It Only works
> well on single core.
>
> This is the warning when I grompp:
> ----------------------
> WARNING 1 [file grompp.mdp]:
> The sum of the two largest charge group radii (16.834835) is larger than
> rlist (1.200000)
> --------------------
>
> This is the error message if i run mdrun using more than 1 core:
> --------------------
> WARNING: Listed nonbonded interaction between particles 8512 and 8550
> at distance 3f which is larger than the table limit 3f nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> A list of missing interactions:
> Bond of 13260 missing 385
> U-B of 25500 missing 1322
> LJ-14 of 37332 missing 1685
>
> Molecule type 'ICE'
> the first 10 missing interactions, except for exclusions:
> Bond atoms 110387 global 1 10387
> U-B atoms 1 58810382 global 1 588 10382
> U-B atoms 110387 575 global 1 10387 575
> LJ-14 atoms 1 593 global 1 593
> LJ-14 atoms 1 596 global 1 596
> LJ-14 atoms 1 598 global 1 598
> LJ-14 atoms 110385 global 1 10385
> U-B atoms 2 589 1185 global 2 589 1185
> U-B atoms 2 1209 576 global 2 1209 576
> LJ-14 atoms 2 599 global 2 599
>
> Back Off! I just backed up dd_dump_err_0_n8.pdb to
> ./#dd_dump_err_0_n8.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n21.pdb to
> ./#dd_dump_err_0_n21.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n14.pdb to
> ./#dd_dump_err_0_n14.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n5.pdb to
> ./#dd_dump_err_0_n5.pdb.1#
>
> Back Off! I just backed up dd_dump_err_0_n1.pdb to
> ./#dd_dump_err_0_n1.pdb.3#
> ...
>
> ---------------------------------------------------------------------------------
> I am wondering if it is because i did not assign charge group for this
> large surface.
>
> Thanks a lot for your suggestions!
>
> Thom
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 15 Mar 2014 18:04:07 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] NVT problem
> Message-ID: <5324CE57.5020207 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/15/14, 5:29 PM, Andres Ortega Guerrero wrote:
> > Hi Justin,
> >
> > I have done a 1ns MD with DOX + water + CL ion , the topology didn?t
> present any problem,
> >
> > i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when i
> was trying to do my nvt.mdp
> >
> > Step 0, time 0 (ps) LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.003859, max 0.176655 (between atoms 47397 and 47398)
> > bonds that rotated more than 30 degrees:
> >
> > WARNING: Listed nonbonded interaction between particles 7156 and 7175
> > at distance 3f which is larger than the table limit 3f nm.
> >
> > IMPORTANT: This should not happen in a stable simulation, so there is
> > probably something wrong with your system. Only change the
> table-extension
> > distance in the mdp file if you are really sure that is the reason.
> >
> > this are the warning that appear, so based on this, the main problem
> seems like to be my structure right?
> > maybe, the DOX is misplaced or something like that, so should i prepare
> again the .gro files?
> >
>
> Yes, if the simulation crashes at step 0 there are severe problems with the
> structure. The error messages tell you the problematic atoms, so simple
> visualization should tell you what is going on.
>
> -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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 15 Mar 2014 18:04:56 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem of running multiple cores
> Message-ID: <5324CE88.3030102 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 3/15/14, 5:55 PM, Tom wrote:
> > Dear Gromacs Users
> >
> > I created a Silca surface with PBC bonding with the image atoms and
> assigned
> > all the intramolecular potentials.
> >
> > It is strange that the generated *tpr can not be run with Multiple cores.
> > It Only works
> > well on single core.
> >
> > This is the warning when I grompp:
> > ----------------------
> > WARNING 1 [file grompp.mdp]:
> > The sum of the two largest charge group radii (16.834835) is larger
> than
> > rlist (1.200000)
> > --------------------
> >
> > This is the error message if i run mdrun using more than 1 core:
> > --------------------
> > WARNING: Listed nonbonded interaction between particles 8512 and 8550
> > at distance 3f which is larger than the table limit 3f nm.
> >
> > This is likely either a 1,4 interaction, or a listed interaction inside
> > a smaller molecule you are decoupling during a free energy calculation.
> > Since interactions at distances beyond the table cannot be computed,
> > they are skipped until they are inside the table limit again. You will
> > only see this message once, even if it occurs for several interactions.
> >
> > IMPORTANT: This should not happen in a stable simulation, so there is
> > probably something wrong with your system. Only change the
> table-extension
> > distance in the mdp file if you are really sure that is the reason.
> >
> > A list of missing interactions:
> > Bond of 13260 missing 385
> > U-B of 25500 missing 1322
> > LJ-14 of 37332 missing 1685
> >
> > Molecule type 'ICE'
> > the first 10 missing interactions, except for exclusions:
> > Bond atoms 110387 global 1 10387
> > U-B atoms 1 58810382 global 1 588 10382
> > U-B atoms 110387 575 global 1 10387 575
> > LJ-14 atoms 1 593 global 1 593
> > LJ-14 atoms 1 596 global 1 596
> > LJ-14 atoms 1 598 global 1 598
> > LJ-14 atoms 110385 global 1 10385
> > U-B atoms 2 589 1185 global 2 589 1185
> > U-B atoms 2 1209 576 global 2 1209 576
> > LJ-14 atoms 2 599 global 2 599
> >
> > Back Off! I just backed up dd_dump_err_0_n8.pdb to
> > ./#dd_dump_err_0_n8.pdb.1#
> >
> > Back Off! I just backed up dd_dump_err_0_n21.pdb to
> > ./#dd_dump_err_0_n21.pdb.1#
> >
> > Back Off! I just backed up dd_dump_err_0_n14.pdb to
> > ./#dd_dump_err_0_n14.pdb.1#
> >
> > Back Off! I just backed up dd_dump_err_0_n5.pdb to
> > ./#dd_dump_err_0_n5.pdb.1#
> >
> > Back Off! I just backed up dd_dump_err_0_n1.pdb to
> > ./#dd_dump_err_0_n1.pdb.3#
> > ...
> >
> ---------------------------------------------------------------------------------
> > I am wondering if it is because i did not assign charge group for this
> > large surface.
> >
>
> Did you use "periodic_molecules = yes" in the .mdp file?
>
> -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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 15 Mar 2014 22:31:46 +0000
> From: Andres Ortega Guerrero <og_andres15 at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] NVT problem
> Message-ID: <BLU181-W37602937A79A7C4F78825E93730 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks Justin for all your Help, i?m going to do all you suggesta and
> prepare a new structure,
> but before that i would like to try with a POSRE for the protein 10000 due
> to i am using 1000,
> also i would like to tell you, that due to the channel , is too big, in
> order to embebed in a 512 POPC Box,
> i deleted some residues located at the terminal (inside the membrane) ,
> so i think this could be
> one reasson of the problem.
>
> Thanks again,
>
> Thanks Andres Ortega
>
> > Date: Sat, 15 Mar 2014 18:04:07 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] NVT problem
> >
> >
> >
> > On 3/15/14, 5:29 PM, Andres Ortega Guerrero wrote:
> > > Hi Justin,
> > >
> > > I have done a 1ns MD with DOX + water + CL ion , the topology didn?t
> present any problem,
> > >
> > > i also did what you suggested, a -DFLEXIBLE EM and settle EM, but when
> i was trying to do my nvt.mdp
> > >
> > > Step 0, time 0 (ps) LINCS WARNING
> > > relative constraint deviation after LINCS:
> > > rms 0.003859, max 0.176655 (between atoms 47397 and 47398)
> > > bonds that rotated more than 30 degrees:
> > >
> > > WARNING: Listed nonbonded interaction between particles 7156 and 7175
> > > at distance 3f which is larger than the table limit 3f nm.
> > >
> > > IMPORTANT: This should not happen in a stable simulation, so there is
> > > probably something wrong with your system. Only change the
> table-extension
> > > distance in the mdp file if you are really sure that is the reason.
> > >
> > > this are the warning that appear, so based on this, the main problem
> seems like to be my structure right?
> > > maybe, the DOX is misplaced or something like that, so should i
> prepare again the .gro files?
> > >
> >
> > Yes, if the simulation crashes at step 0 there are severe problems with
> the
> > structure. The error messages tell you the problematic atoms, so simple
> > visualization should tell you what is going on.
> >
> > -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
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> End of gromacs.org_gmx-users Digest, Vol 119, Issue 68
> ******************************************************
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