[gmx-users] gromacs.org_gmx-users Digest, Vol 124, Issue 40

Sat Aug 9 22:17:10 CEST 2014

Dear Dr. Justin

Thank you for the insight . My problem is solved.

Best

Agnivo Gosai
Graduate Student
Mechanical Engineering
Iowa State University

On Sat, Aug 9, 2014 at 5:00 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>    1. Re: Charmm to gromacs (Justin Lemkul)
>    2. Re: Can I delete trr file? (Justin Lemkul)
>    3. Re: Can we set the number of pure PME nodes when using
>       GPU&CPU? (Theodore Si)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 09 Aug 2014 03:39:07 -0600
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charmm to gromacs
> Message-ID: <53E5EC3B.4070908 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 8/8/14, 9:18 PM, Abu Naser wrote:
> >
> >
> >
> > Thanks Justin for your response.
> >
> > I just manually inserted the input values only to that part of the
> script.  The atom types I am interested in, they are not available in the
> charmm36. Since I have only few unusual atom types, I wish to do them
> manually and trying to figure out how it can be converted.
> >
>
> It appears that the script uses the C6/C12 approach instead of specifying
> sigma
> and epsilon.  That is not how we converted the CHARMM36 files.  The
> conversion
> factors are a simple matter of units.  Epsilon is in kcal/mol and needs to
> be in
> kJ/mol, so multiply by 4.184 (and by -1 since CHARMM specifies these
> values as
> negative, but Gromacs uses a different convention).  For sigma, CHARMM
> specifies
> Rmin/2 directly, but can be converted by multiplying by 2 (to get Rmin),
> then
> multiplying by 2^(-1/6) (to get sigma), then multiplying by 0.1 (to
> convert A->nm).
>
> -Justin
>
> >
> >
> >
> >
> >
> >
> >
> >
> >> Date: Fri, 8 Aug 2014 08:50:16 -0600
> >> From: jalemkul at vt.edu
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Charmm to gromacs
> >>
> >>
> >>
> >> On 8/8/14, 3:11 AM, Abu Naser wrote:
> >>> Hi All,
> >>>
> >>> I took the following from Mark's script to convert non-bonded
> parameters of ZN manually:
> >>>
> >>> printf("% 5s %f   0.0     A %.4g %.4g\n", $atom, $element_mass,
> 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12);
> >>>
> >>>
> >>> I am getting:
> >>>
> >>> -0.0002245 -1.205e-08
> >>>
> >>> instead of:
> >>>
> >>> 0.194215920555  1.046
> >>>
> >>>
> >>> Am I missing anything?
> >>>
> >>> I would appreciate your respond.
> >>>
> >>
> >> Probably something wrong with your input file.  There's no need to do
> these
> >> conversions; we provide the latest CHARMM36 FF for Gromacs at
> >> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> >>
> >> -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.
> >
> >
>
> --
> ==================================================
>
> 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: 2
> Date: Sat, 09 Aug 2014 03:40:17 -0600
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org, Batdorj Batsaikhan
>         <batsaikhanbat at yahoo.com>
> Subject: Re: [gmx-users] Can I delete trr file?
> Message-ID: <53E5EC81.2070508 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote:
> > Dear gmx users,
> >
> > I am new user of gromacs. Our calculations are running, but we have a
> problem that has not enough disk space. Therefore I need to delete some
> file that are unimportant for analysis. Is there any analysis use trr file?
> Can I delete trr file?
> >
>
> Not while mdrun is running; that will kill the run.  The most important
> part of
> the run is the trajectory, so if you delete the .trr you'd better have the
> .xtc
> as well, otherwise there was no point in doing the simulation.  Better
> planning
> (in terms of frequency for saving frames) and paying attention to what
> grompp
> tells you about how much data will be generated pay off here.
>
> -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: 3
> Date: Sat, 09 Aug 2014 17:56:47 +0800
> From: Theodore Si <sjyzhxw at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Can we set the number of pure PME nodes when
>         using GPU&CPU?
> Message-ID: <53E5F05F.70507 at gmail.com>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hi,
>
> You mean no matter we use GPU acceleration or not, -npme is just a
> reference?
> Why we can't set that to a exact value?
>
> On 8/9/2014 5:14 AM, Mark Abraham wrote:
> > You can set the number of PME-only ranks with -npme. Whether it's useful
> is
> > another matter :-) The CPU-based PME offload and the GPU-based PP offload
> > do not combine very well.
> >
> > Mark
> >
> >
> > On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si <sjyzhxw at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> Can we set the number manually with -npme when using GPU acceleration?
> >>
> >>
> >> --
> >> 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 124, Issue 40
> ******************************************************
>