[gmx-users] gromacs.org_gmx-users Digest, Vol 125, Issue 59

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Sep 12 21:41:14 CEST 2014 

Dear Chris

Thanks for suggesting Propka.

Regards
Agnivo.

On Fri, Sep 12, 2014 at 12:28 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: Using GROMACS to find the net charge on a Protein
>       (donna at iflysib.unlp.edu.ar)
>    2. mpi/openmp setup to avoid #1578 on 5.0 (Johnny Lu)
>    3. Re: talk page on gromacs wiki (Johnny Lu)
>    4. Re: Regargding simulation of periodic silica surface (Mirco Wahab)
>    5. Re: mpi/openmp setup to avoid #1578 on 5.0 (Szil?rd P?ll)
>    6. Re: mpi/openmp setup to avoid #1578 on 5.0 (Johnny Lu)
>    7. Re: Problems with the force field (jvissoto at fisica.ufpr.br)
>
>
> ---------- Forwarded message ----------
> From: donna at iflysib.unlp.edu.ar
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 12 Sep 2014 11:14:50 -0300
> Subject: Re: [gmx-users] Using GROMACS to find the net charge on a Protein
> Dear Agnivo
>
> Regarding your inquiry: there is an online tool to determine the pka value
> of a protein (of its aminoacids) if you have the pdb file of your protein
>  The program is "Propka " see it at internet ,( See the paper" "Very Fast
> Empirical Prediction and Rationalization of Protein pKa Values"de Hui Li,
> Andrew D. Robertson and  Jan H. Jensen,  in PROTEINS: Structure, Function,
> and Bioinformatics 61:704 ?721 (2005))
>
> You should look if the pH, which you need,  is > o < that the corresponding
> value of pka and then you should determine  the protonation state of the
> protein . The pdb2gmx program has the option of being interactive with
> respect to those aminoacids that have negative or positive charge depending
> of its pka
> and the PH ( Glu.Asp, lys, Arg and hys).See that hys at physiological pH
> has no charge.
>  Best Regards,
>      Chris
>
>
>
> Agnivo Gosai <agnivo2007 at gmail.com> ha escrito:
>
>  Dear Users
>>
>> I am trying to find the net charge at the physiological pH value for a
>> protein molecule (Thrombin) in my case and am wondering if it is possible
>> to use GROMACS for doing it.
>>
>> I am very new to GROMACS and at present I have been going through the
>> tutorials by Dr. Lemkul. I have seen that the topology file generated by
>> "pdb2gmx" contains the total electron charge value for a molecule.
>>
>> I was wondering if this can be used to get the charge value for Thrombin
>> at
>> physiological pH.
>>
>> Thanks & Regards
>>
>> Agnivo Gosai
>> Graduate Student
>> Mechanical Engineering
>> Iowa State University
>> --
>> Gromacs Users mailing list
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>
> ---------- Forwarded message ----------
> From: Johnny Lu <johnny.lu128 at gmail.com>
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 12 Sep 2014 11:36:52 -0400
> Subject: [gmx-users] mpi/openmp setup to avoid #1578 on 5.0
> Hi.
> I wonder if I run with following, will I get bug 1578 of gromacs 5.0?
>
> The number of OpenMP threads was set by environment variable
> OMP_NUM_THREADS to 1
> Using 12 MPI processes
> Using 1 OpenMP thread per MPI process
>
> And, is it ok to use tpr of version 5.0.1 double precision on gromacs 5.0
> double precision?
>
> I have 5.0.1 on one machine, but 5.0 on another machine.
>
> By the way, would gromacs 5.0.1 single precision with GPU have nearly as
> little truncation error (like cutting 3.212 to 3.2) as the double precision
> version, in NVE simulation?
>
>
>
> ---------- Forwarded message ----------
> From: Johnny Lu <johnny.lu128 at gmail.com>
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 12 Sep 2014 11:37:33 -0400
> Subject: Re: [gmx-users] talk page on gromacs wiki
> My username on wiki is:
>
> User name: johnny.lu128
>
> On Fri, Sep 12, 2014 at 9:10 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > We're happy to give people editing rights - please drop Rossen or I an
> > email and let us know your account name. We just can't leave it open
> > because we'll get graffittied.
> >
> > Mark
> >
> >
> > On Fri, Sep 12, 2014 at 2:27 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> > > Hi. Is it a good idea to open the talk page on gromacs wiki for
> everyone
> > to
> > > edit, just to record the rumors and common practice (Or, we can already
> > > edit that wiki?) ?
> > > --
> > > 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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> >
>
>
>
> ---------- Forwarded message ----------
> From: Mirco Wahab <mirco.wahab at chemie.tu-freiberg.de>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc:
> Date: Fri, 12 Sep 2014 17:42:33 +0200
> Subject: Re: [gmx-users] Regargding simulation of periodic silica surface
> On 12.09.2014 16:16, Sathish Kumar wrote:
>
>> So in SiO2 structure atoms are getting merged, is that the reason for the
>> error in simulation?
>>
>
> Aside from the y-PBC overlap, please look closer into
> your coordinates:
>
> ...
> ...
> 1882MAK     Si 1710   6.303   0.003   4.160
> ...
> ...
> ...
> 4480SOB     BO 6359   6.303   0.003   4.160
> ...
> ...
>
> Where did you get these coordinates from? They seem
> to need another cleanup and preprocessing step before
> simulation.
>
> Regards
>
> M.
>
>
>
>
>
> ---------- Forwarded message ----------
> From: "Szilárd Páll" <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Date: Fri, 12 Sep 2014 18:10:08 +0200
> Subject: Re: [gmx-users] mpi/openmp setup to avoid #1578 on 5.0
> On Fri, Sep 12, 2014 at 5:36 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> > Hi.
> > I wonder if I run with following, will I get bug 1578 of gromacs 5.0?
> >
> > The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 1
> > Using 12 MPI processes
> > Using 1 OpenMP thread per MPI process
>
> No, as the redmine message states "Note that without OpenMP threads
> there are no issues." (i.e. single thread per rank). Unfortunately the
> redmine auto-update mechanism is not working correctly and the actual
> change that fixed it (6ba80a from Aug 15) did not show up on the
> redmine page. This change is included in the 5.0.1 release.
>
> > And, is it ok to use tpr of version 5.0.1 double precision on gromacs 5.0
> > double precision?
>
> Yes, that should work.
>
> > I have 5.0.1 on one machine, but 5.0 on another machine.
> >
> > By the way, would gromacs 5.0.1 single precision with GPU have nearly as
> > little truncation error (like cutting 3.212 to 3.2) as the double
> precision
> > version, in NVE simulation?
>
> No, but truncation is, typically not a big issue - unless you have a
> very large system (where differences in coordinates can be coordinates
> can be 2-3 orders of magnitude).
>
> --
> Szilárd
>
> > --
> > 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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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
>
> ---------- Forwarded message ----------
> From: Johnny Lu <johnny.lu128 at gmail.com>
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 12 Sep 2014 13:03:11 -0400
> Subject: Re: [gmx-users] mpi/openmp setup to avoid #1578 on 5.0
> Thanks for the quick mail.
>
> If I use 20 openmp threads and 1 MPI rank, will that bug happen in gromacs
> 5.0 (not 5.0.1)?
>
>
>
>
> On Fri, Sep 12, 2014 at 12:10 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > On Fri, Sep 12, 2014 at 5:36 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> > > Hi.
> > > I wonder if I run with following, will I get bug 1578 of gromacs 5.0?
> > >
> > > The number of OpenMP threads was set by environment variable
> > > OMP_NUM_THREADS to 1
> > > Using 12 MPI processes
> > > Using 1 OpenMP thread per MPI process
> >
> > No, as the redmine message states "Note that without OpenMP threads
> > there are no issues." (i.e. single thread per rank). Unfortunately the
> > redmine auto-update mechanism is not working correctly and the actual
> > change that fixed it (6ba80a from Aug 15) did not show up on the
> > redmine page. This change is included in the 5.0.1 release.
> >
> > > And, is it ok to use tpr of version 5.0.1 double precision on gromacs
> 5.0
> > > double precision?
> >
> > Yes, that should work.
> >
> > > I have 5.0.1 on one machine, but 5.0 on another machine.
> > >
> > > By the way, would gromacs 5.0.1 single precision with GPU have nearly
> as
> > > little truncation error (like cutting 3.212 to 3.2) as the double
> > precision
> > > version, in NVE simulation?
> >
> > No, but truncation is, typically not a big issue - unless you have a
> > very large system (where differences in coordinates can be coordinates
> > can be 2-3 orders of magnitude).
> >
> > --
> > Szilárd
> >
> > > --
> > > 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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>
>
>
> ---------- Forwarded message ----------
> From: jvissoto at fisica.ufpr.br
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 12 Sep 2014 14:20:20 -0300 (BRT)
> Subject: Re: [gmx-users] Problems with the force field
>
> Dear Terry
>
> I have looked in several places and could not find any author who has
> explained this procedure to force fields in conjugated polymers.
> Currently, I simulate with the OPLS force field (for alkenes / alkanes)
> but I do not know if this application is correct for polyacetylene.
>
> Thanks for all
>
> Best regards
>
> Jeniffer
>
>
> _______________________________________________-
> > Hi, Jeniffer,
> >
> > I've never simulated polyacetylene. But the common approach starts with
> > literature research. See what force field others used.
> >
> > Terry
> >
> > On Fri, Sep 12, 2014 at 9:11 AM, <jvissoto at fisica.ufpr.br> wrote:
> >
> >> Hello,
> >>
> >> My name is Jeniffer and i'm having some trouble to find the correct
> >> force
> >> field to put in my MD simulation using GROMACS. I'm working with a
> >> molecule of polyacetylene "trans" in vacuum and i would appreciate if
> >> you
> >> could indicate me the correct force field for this molecule.
> >>
> >> Thanks for all
> >>
> >> Best regards
> >>
> >> Jeniffer
> >>
> >>
> >> --
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
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>
>
>
>
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