[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul)

Wed Feb 18 17:50:52 CET 2015

Dear Justin,

We thought about this, and checked these non-crashed lambda tpr as well as
the pre-equilbrated NPT step, all showed mismatch between posre-com[0]
posre-com[1] posre-com[2], and the real com. So I suspect this posre-com is
not the real center of mass for NPT simulation.
Since the reference coordinate is read from -c .gro when perform grompp, it
should not be wrong, unless it read elsewhere.

Best,
Jin

> Date: Wed, 18 Feb 2015 07:42:30 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] free energy calculation: combination of
>         position restraint +refcoord_scaling cause crash during NPT
> Message-ID: <54E488B6.9090300 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/17/15 12:31 PM, Jin Zhang wrote:
> > Dear all,
> >
> > We're doing free energy calculation and found some of my lambda job
> crashes
> > due to the combination of position restraint +refcoord_scaling COM. All
> > crashes happened at NPT steps.
> >
> > By checking each energy term, we found the Position Rest. term is
> > surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
> > position restrain or refcoord_scaling could avoid the simulation to be
> > crashed. We tried to see if there's mismatch of either COM or coordinate
> > and found no direct answer.
> > Any help would be appreciated!
> >
> > In the tpr file
> >        refcoord-scaling     = COM
> >        posres-com (3):
> >        posres-com[0]= 3.15034e-01
> >        posres-com[1]= 4.48110e-01
> >        posres-com[2]= 5.17730e-01
> >
> > COM of protein-ligand calculated by t_traj -com -ox
> > 3.02422    4.30169    4.84964
> >
>
> If the reference COM is defined as (0.315,0.448,0.518) and your actual
> coordinates are what you're shown above, there will inherently be a huge
> restraint potential as mdrun tries to bias the coordinates towards the
> defined
> reference.  I suspect something is wrong in your definition of your
> reference.
>
> -Justin
>
> > coordinate of 1st atom in tpr: posres_xA[    0]={ 1.39783e-01,
> > -9.56922e-02,  1.22536e+00}
> > coordinate of 1st atom in gro:     1MOL     C1    1   3.164   4.206
> > 6.075
> >
> > The same thing was also found in a normal non-free energy simulations
> with
> > combination of position restrain and refcoord-scaling.
> > Later on, we found some other people also have the same problem when use
> > that combination to do free energy calculation.
> > http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
> > It makes more sense to me to turn on refcoord_scaling while using
> position
> > restraint.
> > Again, any help to understand this would be appreciated!
> >
> > Regards,
> > Jin
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 18 Feb 2015 19:48:50 +0530
> From: Sanchaita Rajkhowa <srajkhowa18 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] simulation of heme along with h2o2
> Message-ID:
>         <CACE5zdsaXX==in=SPntZiaRZ=+
> nRJnyajN8UwMMWYSVsR4xrKA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all, I am trying to simulate a heme containing protein in high
> concentration (having hydrogen peroxide). However, I do not know which
> forcefield to use. Heme has forcefield in gromos96 but not the forcefield
> of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
> help.
>
> Thanks in advance.
> Sanchaita.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 18 Feb 2015 16:30:34 +0100
> From: "Carmen Di Giovanni" <cdigiova at unina.it>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] GPU low performance
> Message-ID: <8525B4BE52BB4609BCED7556FAFB3587 at PCCarmen>
> Content-Type: text/plain;       charset="iso-8859-1"
>
> Daear all,
> I'm working on a machine with an INVIDIA Teska K20.
> After a minimization on a protein of 1925 atoms this is the mesage:
>
> Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
> For optimal performance this ratio should be close to 1!
>
>
> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
> performance loss.
>
> Core t (s) Wall t (s) (%)
> Time: 3289.010 205.891 1597.4
> (steps/hour)
> Performance: 8480.2
> Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
>
>
> Cai I improve the performance?
> At the moment in the forum I didn't full informations to solve this
> problem.
> In attachment there is the log. file
>
> thank you in advance
> Carmen Di Giovanni
>
>
> --
> Carmen Di Giovanni, PhD
> Dept. of Pharmaceutical and Toxicological Chemistry
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigiova at unina.it
>
>
> Carmen Di Giovanni, PhD
> Postdoctoral Researcher
> Dept. of Pharmacy
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigiova at unina.it
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 18 Feb 2015 10:45:14 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation of heme along with h2o2
> Message-ID: <54E4B38A.3040601 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote:
> > Dear all, I am trying to simulate a heme containing protein in high
> > concentration (having hydrogen peroxide). However, I do not know which
> > forcefield to use. Heme has forcefield in gromos96 but not the forcefield
> > of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
> > help.
> >
>
> SwissParam creates CHARMM-compatible parameters, so no, you can't mix
> those with
> GROMOS.  CHARMM supports heme, but you have to clean up a lot of
> auto-generated
> angles and dihedrals that don't belong.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 18 Feb 2015 10:46:29 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GPU low performance
> Message-ID: <54E4B3D5.6070707 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/18/15 10:30 AM, Carmen Di Giovanni wrote:
> > Daear all,
> > I'm working on a machine with an INVIDIA Teska K20.
> > After a minimization on a protein of 1925 atoms this is the mesage:
> >
> > Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
> > For optimal performance this ratio should be close to 1!
> >
>
> Minimization is a poor indicator of performance.  Do a real MD run.
>
> >
> > NOTE: The GPU has >25% less load than the CPU. This imbalance causes
> > performance loss.
> >
> > Core t (s) Wall t (s) (%)
> > Time: 3289.010 205.891 1597.4
> > (steps/hour)
> > Performance: 8480.2
> > Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
> >
> >
> > Cai I improve the performance?
> > At the moment in the forum I didn't full informations to solve this
> problem.
> > In attachment there is the log. file
> >
>
> The list does not accept attachments.  If you wish to share a file, upload
> it to
> a file-sharing service and provide a URL.  The full .log is quite
> important for
> understanding your hardware, optimizations, and seeing full details of the
> performance breakdown.  But again, base your assessment on MD, not EM.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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 130, Issue 75
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