[gmx-users] Re: gmx-users Digest, Vol 115, Issue 16
Stephanie Teich-McGoldrick
stephanietm at gmail.com
Wed Nov 6 01:14:45 CET 2013
Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <5277E854.9000305 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Justin,
Thanks for the response. My question was prompted by line 243 in
gmx_cluster.c which states "/* Should use pbc_dx when analysing multiple
molecueles,but the box is not stored for every frame.*/" I just wanted to
verify that analysis tools are written for any box shape.
Cheers,
Stephanie
On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote:
> Dear all,
>
> I am using gromacs 4.6.3 with a triclinic box. Based on the manual and
mail
> list, it is my understanding that the default box shape in gromacs in a
> triclinic box. Can I assume that all the analysis tools also work for a
> triclinic box.
>
All analysis tools should work correctly for all box types. Is there a
specific
issue you are having, or just speculation?
-Justin
--
==============================
====================
Justin A. Lemkul, Ph.D.
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
==================================================
On Mon, Nov 4, 2013 at 12:28 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: Re: Installation Gromacs 4.5.7 on rocluster cluster with
> centos 6.0 (Mark Abraham)
> 2. Analysis tools and triclinic boxes (Stephanie Teich-McGoldrick)
> 3. Group protein not found in indexfile (Steve Seibold)
> 4. Re: Group protein not found in indexfile (Justin Lemkul)
> 5. Re: Analysis tools and triclinic boxes (Justin Lemkul)
> 6. Re: TFE-water simulation (Archana Sonawani-Jagtap)
> 7. Re: Gentle heating with implicit solvent (Gianluca Interlandi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Nov 2013 17:05:36 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster
> cluster with centos 6.0
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAMNuMAQcWLcKA=GPG1Ewr8s4A=PoTGOSWaqa=
> S_uZbYW8UfVZw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta <bharat.85.monu at gmail.com
> >wrote:
>
> > Hi,
> >
> > I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works
> > fine till .configure command, but I am getting error at the make command
> :-
> >
> > Error:
> > ====================
> > [root at cluster gromacs-4.5.7]# make
> >
>
> These is no need to run make as root - doing so guarantees you have almost
> no knowledge of the final state of your entire machine.
>
>
> > /bin/sh ./config.status --recheck
> > running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi
> > LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create
> > --no-recursion
> > checking build system type... x86_64-unknown-linux-gnu
> > checking host system type... x86_64-unknown-linux-gnu
> > ./configure: line 2050: syntax error near unexpected token `tar-ustar'
> > ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)'
> > make: *** [config.status] Error 2
> >
>
> Looks like the system has an archaic autotools setup. Probably you can
> comment out the line with tar-ustar from the original configure script, or
> remove tar-ustar. Or use the CMake build.
>
>
> >
> >
> > I have another query regarding the gromacs that comes with the Rocks
> > cluster distribution. The mdrun of that gromacs has been complied without
> > mpi option. How can I recomplie with mpi option. As I need the .configure
> > file which is not there in the installed gromacs folder of the rocks
> > cluster ...
> >
>
> The 4.5-era GROMACS installation instructions are up on the website.
> Whatever's distributed with Rocks is more-or-less irrelevant.
>
> Mark
>
>
> >
> >
> > Thanks in advance for help
> >
> >
> >
> >
> > Regards
> > ------------
> > Bharat
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 4 Nov 2013 11:29:43 -0700
> From: Stephanie Teich-McGoldrick <stephanietm at gmail.com>
> Subject: [gmx-users] Analysis tools and triclinic boxes
> To: gmx-users at gromacs.org
> Message-ID:
> <CAF3rbpYDH-79tjESREDNzxJHSdGTV9q6=m+v=
> C3aSVwSEOPSyw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>
> I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail
> list, it is my understanding that the default box shape in gromacs in a
> triclinic box. Can I assume that all the analysis tools also work for a
> triclinic box.
>
> Cheers,
> Stephanie
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 4 Nov 2013 10:29:06 -0800 (PST)
> From: Steve Seibold <stevesei at ymail.com>
> Subject: [gmx-users] Group protein not found in indexfile
> To: gmx-users at gromacs.org
> Message-ID:
> <1383589746.69990.YahooMailBasic at web140503.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
> Hello
> I am just trying to do a simple MD on a dimmer system (in which the
> dimmers are NOT identical). I can use pdb2gmx to create a topology file and
> four .itp files:::: pores.chainA.itp, pores.chainX.itp;
> system.Protein.chainA.itp and system.Protein.chainX.itp.
>
> When I use grompp however, I get a fatal error “Group protein not found
> in index file. Maybe you have non-default groups in your .mdp file, while
> not using ‘-n’ option in grompp”
>
> I’ve looked up this error on-line but I don’t see people getting this
> error when using multiple chains. I only have protein present and nothing
> else. I am obviously doing something incorrect.
>
> I would greatly appreciate any comments that would help me..
>
> Thanks.
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 04 Nov 2013 13:32:22 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Group protein not found in indexfile
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <5277E836.6050302 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 11/4/13 1:29 PM, Steve Seibold wrote:
> > Hello
> > I am just trying to do a simple MD on a dimmer system (in which the
> dimmers are NOT identical). I can use pdb2gmx to create a topology file and
> four .itp files:::: pores.chainA.itp, pores.chainX.itp;
> system.Protein.chainA.itp and system.Protein.chainX.itp.
> >
> > When I use grompp however, I get a fatal error “Group protein not found
> in index file. Maybe you have non-default groups in your .mdp file, while
> not using ‘-n’ option in grompp”
> >
> > I’ve looked up this error on-line but I don’t see people getting this
> error when using multiple chains. I only have protein present and nothing
> else. I am obviously doing something incorrect.
> >
> > I would greatly appreciate any comments that would help me..
> >
>
> Please provide:
>
> 1. Your exact grompp command
> 2. Your full .mdp file
> 3. The gmxcheck output of the .ndx file
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 04 Nov 2013 13:32:52 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Analysis tools and triclinic boxes
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <5277E854.9000305 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote:
> > Dear all,
> >
> > I am using gromacs 4.6.3 with a triclinic box. Based on the manual and
> mail
> > list, it is my understanding that the default box shape in gromacs in a
> > triclinic box. Can I assume that all the analysis tools also work for a
> > triclinic box.
> >
>
> All analysis tools should work correctly for all box types. Is there a
> specific
> issue you are having, or just speculation?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 5 Nov 2013 00:25:38 +0530
> From: Archana Sonawani-Jagtap <ask.archana at gmail.com>
> Subject: Re: [gmx-users] TFE-water simulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <
> CAFV47mi+M372DPQYCQzpdsgyg+Y7rdMPBfGq5C4D9BMpLLYSQQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks Joao Henriques for helping me with the steps.
> On Nov 4, 2013 3:18 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
> wrote:
>
> > Hello Archana,
> >
> > I'm also toying with a TFE-water system, therefore I am also a newbie.
> This
> > is what I am doing, I hope it helps:
> >
> > 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I
> > don't use PRODGR, see why in DOI: 10.1021/ci100335w).
> > 2) Do the math and check how many molecules of TFE you're going to need
> for
> > a given v/v TFE-water ratio and a given simulation box volume.
> > 3) Build box with the correct size.
> > 4) Randomly insert correct number of TFE molecules.
> > 5) Solvate.
> > 6) Insert protein.
> >
> > Hopefully, the amount of TFE and water molecules that will be deleted in
> > inserting the protein in the final step will be proportional, given that
> > the TFE molecules are well distributed.
> >
> > I've tried many different ways of doing this and it's always impossible
> to
> > maintain a perfect TFE-water ratio, no matter the order and manner of
> > insertion of each system component. I've also never been able to insert
> the
> > correct number of waters after the TFE. My calculations predict a higher
> > number, but the solvation algorithm can't find enough space for them.
> >
> > In sum, either you place each molecule by hand and you spend a life time
> > building the system, or you just make a few compromises and deal with
> it. I
> > ended up going with the former as I have a limited amount of time on my
> > hands and I am aware of the approximations I am doing.
> >
> > Best regards,
> >
> > João Henriques
> > ------------------------------------------------
> > PhD student
> > Division of Theoretical Chemistry
> > Lund University
> > Lund, Sweden
> > ------------------------------------------------
> > joao.henriques at teokem.lu.se
> > http://www.teokem.lu.se/~joaoh/
> >
> >
> > On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote:
> > >
> > >> Dear Justin,
> > >>
> > >> I have not constructed the system but I have downloaded it from ATB
> > >> website. To maintain the number of TFE and water molecules(1:1 v/v) in
> > the
> > >> system (I don't want to add extra water molecules) I tried many
> options
> > in
> > >> genbox but still it adds 678 water molecules. Can you provide me some
> > >> hint?
> > >>
> > >>
> > > Not without seeing your actual command(s).
> > >
> > >
> > > Is their need to remove periodicity of this pre-equilibrated system as
> > in
> > >> case of lipids?
> > >>
> > >>
> > > No idea. Are the molecules broken in the initial configuration?
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > >
> > > Justin A. Lemkul, Ph.D.
> > > 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
> > >
> > > ==================================================
> > >
> > > --
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-request at gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 4 Nov 2013 11:25:32 -0800 (PST)
> From: Gianluca Interlandi <gianluca at u.washington.edu>
> Subject: Re: [gmx-users] Gentle heating with implicit solvent
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <
> alpine.LNX.2.00.1311041112100.17841 at artemide.bioeng.washington.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Dear Mark,
>
> Sorry for replying to an older thread. We are trying to perform implicit
> solvent simulations of protein G with CHARMM27 in gromacs. We are trying
> to trouble shoot why the protein unfolds after already 2 ns of dynamics.
> We use simulated annealing for the heating with 1 fs time step. The
> thermostat is v_rescale and OBC is the GBSA algorithm. Do you have any
> suggestions what we could improve? You mention using a sub-fs time step
> for the equilibration. Do you still use LINCS? Do you use simulated
> annealing to heat up the system or do you just apply position restraints
> to the heavy atoms?
>
> Thanks,
>
> Gianluca
>
> On Wed, 28 Aug 2013, Mark Abraham wrote:
>
> > It can be. Lack of explicit degrees of freedom of solvent can make
> > achieving equipartition tricky. With CHARMM27 and virtual sites in
> implicit
> > solvent, I have sometimes found it necessary to use a sub-femtosecond
> time
> > step at the start of equilibration, even where there were no atomic
> > clashes. Maybe the system was just unlucky with generating velocities,
> > though :-)
> >
> > Mark
> > On Aug 28, 2013 7:16 AM, "Gianluca Interlandi" <
> gianluca at u.washington.edu>
> > wrote:
> >
> >> How important is it to do gentle heating (using simulated annealing)
> with
> >> GBSA? Often with explicit water it is enough to perform some
> equilibration
> >> with positional restraints. Would it be enough to do the same with
> implicit
> >> solvent?
> >>
> >> Thanks,
> >>
> >> Gianluca
> >>
> >> ------------------------------**-----------------------
> >> Gianluca Interlandi, PhD gianluca at u.washington.edu
> >> +1 (206) 685 4435
> >> http://artemide.bioeng.**washington.edu/<
> http://artemide.bioeng.washington.edu/>
> >>
> >> Research Scientist at the Department of Bioengineering
> >> at the University of Washington, Seattle WA U.S.A.
> >> http://healthynaturalbaby.org
> >> ------------------------------**-----------------------
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the www
> >> interface or send it to gmx-users-request at gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >>
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
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> End of gmx-users Digest, Vol 115, Issue 16
> ******************************************
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