[gmx-users] Gromacs output analysis
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 3 20:36:42 CEST 2009
rituraj purohit wrote:
> Hello to everybody
> I need the gromacs analysis document. I mean i want to do analysis
> (like; RMSD, traj)of my result which I got after simulation of protein
> molecule.
> If anybody having any PDF or web link emphasis the analysis part, please
> forword me...
Chapter 8 of the manual contains information on all of the analysis programs.
-Justin
> Thank you
>
>
> Rituraj
>
> On Wed, Jun 3, 2009 at 9:05 PM, <gmx-users-request at gromacs.org
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> Today's Topics:
>
> 1. protein running out of box (sheerychen)
> 2. Re: protein running out of box (Justin A. Lemkul)
> 3. Re: protein running out of box (ravi sharma)
> 4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)
> 5. Some questions regarding generating topologies (Manik Mayur)
> 6. Re: Some questions regarding generating topologies
> (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Jun 2009 15:37:57 +0200
> From: sheerychen <sheerychen at gmail.com <mailto:sheerychen at gmail.com>>
> Subject: [gmx-users] protein running out of box
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <e1b92dfb0906030637y6cc57951oaf959aafd2b46d30 at mail.gmail.com
> <mailto:e1b92dfb0906030637y6cc57951oaf959aafd2b46d30 at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello, every body. I have running a MD for 10ns. However, after 5ns
> part of
> protein will running out of the box and be located at other part of the
> water box. And the whole structure seems ver strange. It seems that
> it was
> caused by the mass translation but I have used the
> comm_mode=Linear. Any
> suggestions?
>
> --
> Zhen Chen,
> Department of Bioprocess and Biosystem Engineering,
> Hamburg University of Technology, Denickestr. 15, D-21071,
> Hamburg,Germany
> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.chen at tuhh.de
> <mailto:zhen.chen at tuhh.de>
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> ------------------------------
>
> Message: 2
> Date: Wed, 03 Jun 2009 09:46:08 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] protein running out of box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4A267EA0.8090308 at vt.edu <mailto:4A267EA0.8090308 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sheerychen wrote:
> > Hello, every body. I have running a MD for 10ns. However, after
> 5ns part
> > of protein will running out of the box and be located at other
> part of
> > the water box. And the whole structure seems ver strange. It
> seems that
> > it was caused by the mass translation but I have used the
> > comm_mode=Linear. Any suggestions?
> >
>
> What you are seeing is a normal consequence of periodicity. There
> is no "side"
> in an infinite system:
>
> http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions
>
> -Justin
>
> > --
> > Zhen Chen,
> > Department of Bioprocess and Biosystem Engineering,
> > Hamburg University of Technology, Denickestr. 15, D-21071,
> Hamburg,Germany
> > Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail:
> zhen.chen at tuhh.de <mailto:zhen.chen at tuhh.de>
> > <mailto:zhen.chen at tuhh.de <mailto:zhen.chen at tuhh.de>>
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT)
> From: ravi sharma <rdsharma_4u at yahoo.com <mailto:rdsharma_4u at yahoo.com>>
> Subject: Re: [gmx-users] protein running out of box
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <147031.55861.qm at web54606.mail.re2.yahoo.com
> <mailto:147031.55861.qm at web54606.mail.re2.yahoo.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Zhen Chen
>
> Protein is located stranger(sometime at the one side of the
> protein,in other frame other side). Its not a problem. Your
> simulation is fine. it is due to you had given PBC. thats why. You
> can reset your trejectory using trjconv.
>
>
> regards
>
> Ravi Datta Sharma Lecturer, Bioinformatics,
> Department of Microbiology,
> CCS Unversity,
> Meerut
>
>
>
> --- On Wed, 3/6/09, sheerychen <sheerychen at gmail.com
> <mailto:sheerychen at gmail.com>> wrote:
>
> From: sheerychen <sheerychen at gmail.com <mailto:sheerychen at gmail.com>>
> Subject: [gmx-users] protein running out of box
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Date: Wednesday, 3 June, 2009, 7:07 PM
>
> Hello, every body. I have running a MD for 10ns. However, after 5ns
> part of protein will running out of the box and be located at other
> part of the water box. And the whole structure seems ver strange. It
> seems that it was caused by the mass translation but I have used
> the comm_mode=Linear. Any suggestions?
>
>
> --
> Zhen Chen,
> Department of Bioprocess and Biosystem Engineering,
> Hamburg University of Technology, Denickestr. 15, D-21071,
> Hamburg,Germany
> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: zhen.chen at tuhh.de
> <mailto:zhen.chen at tuhh.de>
>
>
>
> -----Inline Attachment Follows-----
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 3 Jun 2009 14:43:09 +0000
> From: Rebeca Garc?a Fandi?o <regafan at hotmail.com
> <mailto:regafan at hotmail.com>>
> Subject: [gmx-users] spc.itp for the amber force field
> To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID: <BAY142-W27797B710E741D553D80E4B74A0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> I am trying to simulate a system using the parameters for ions
> developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
>
> I have the topology and the crd file. Now, I want to obtain the
> topology for Gromacs using amb2gmx.pl, so I must change the default
> parameters (for tip3p) included in amb2gmx.pl.
>
> I have seen that in the .tar file ffamber_v4.0 there is no a
> corresponding itp file for spc model of water in amber, so what
> parameters should I include for the section of bondtypes,
> angletypes, atoms, bonds, angles, settles,...? Those corresponding
> to the SCP in Gromacs directly?
>
> Thank you very much for your help.
>
> Best wishes,
>
>
>
> Rebeca Garcia
>
> Academic Visitor
>
> Oxford University
>
> _________________________________________________________________
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> ------------------------------
>
> Message: 5
> Date: Wed, 3 Jun 2009 20:57:57 +0530
> From: Manik Mayur <manik.mayur at gmail.com <mailto:manik.mayur at gmail.com>>
> Subject: [gmx-users] Some questions regarding generating topologies
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <7e56bc410906030827t5c183f2fxb10049788c1b1c85 at mail.gmail.com
> <mailto:7e56bc410906030827t5c183f2fxb10049788c1b1c85 at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> Even though after going through the manual, I still have some basic
> confusions regarding generating topologies.
>
> 1) I have generated an itp file after adding some Cl- ions using
> genion. It
> goes like this:
>
> [ moleculetype ]
> ; Name nrexcl
> Cl_ion 0
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 CL- 1 Cl- Cl 1 -1 35.453
> ; qtot
> -1
> 2 CL- 2 Cl- Cl 2 -1 35.453
> ; qtot
> -2
> 3 CL- 3 Cl- Cl 3 -1 35.453
> ; qtot
> -3
> ........
> ........
>
> To allow nb interactions between all the atoms in the molecule
> Cl_ion, is
> setting nrexcl = 0 okay?
>
> 2) In spce.itp provided with GROMACS,
>
> [ moleculetype ]
> ; molname nrexcl
> SOL 2
>
> while in the manual, on pg. 100 (Chapter-5 Topologies)
> [ moleculetype ]
> ; molname nrexcl
> SOL 1
>
> why is the inconsistency?
>
> 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
> recommended).
> Since SPC/E is one of the most used model, should I consider using OPLS
> rather than GROMOS96, otherwise how significant will be the errors?
>
> 4) I am using GROMOS96 43a1, so am I allowed to change combination
> rule to
> '2' ( '1' is the default). How significantly will it affect the
> simulations?
>
> Any relevant idea/suggestion/reference is appreciated.
>
> Thanks,
>
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> INDIA
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> ------------------------------
>
> Message: 6
> Date: Wed, 03 Jun 2009 11:34:34 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Some questions regarding generating
> topologies
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4A26980A.1000205 at vt.edu <mailto:4A26980A.1000205 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Manik Mayur wrote:
> > Hi,
> >
> > Even though after going through the manual, I still have some basic
> > confusions regarding generating topologies.
> >
> > 1) I have generated an itp file after adding some Cl- ions using
> genion.
> > It goes like this:
> >
>
> This is unnecessary. Just #include "ions.itp" and the parameters
> for Cl- for
> whatever force field you're using are included.
>
> > [ moleculetype ]
> > ; Name nrexcl
> > Cl_ion 0
> >
> > [ atoms ]
> > ; nr type resnr residue atom cgnr charge mass
> > typeB chargeB massB
> > 1 CL- 1 Cl- Cl 1 -1
> 35.453 ;
> > qtot -1
> > 2 CL- 2 Cl- Cl 2 -1
> 35.453 ;
> > qtot -2
> > 3 CL- 3 Cl- Cl 3 -1
> 35.453 ;
> > qtot -3
> > ........
> > ........
> >
> > To allow nb interactions between all the atoms in the molecule
> Cl_ion,
> > is setting nrexcl = 0 okay?
> >
> > 2) In spce.itp provided with GROMACS,
> >
> > [ moleculetype ]
> > ; molname nrexcl
> > SOL 2
> >
> > while in the manual, on pg. 100 (Chapter-5 Topologies)
> > [ moleculetype ]
> > ; molname nrexcl
> > SOL 1
> >
> > why is the inconsistency?
> >
>
> Probably just a typo.
>
> > 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
> > recommended). Since SPC/E is one of the most used model, should I
> > consider using OPLS rather than GROMOS96, otherwise how
> significant will
> > be the errors?
> >
>
> An excellent comparison of different force fields and different
> water models can
> be found in:
>
> Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.
>
> > 4) I am using GROMOS96 43a1, so am I allowed to change
> combination rule
> > to '2' ( '1' is the default). How significantly will it affect the
> > simulations?
> >
>
> I would say it invalidates everything. The defaults for combination
> rules,
> bonded parameters, etc. are as much a part of each force field as
> the atom types
> and charges.
>
> -Justin
>
> > Any relevant idea/suggestion/reference is appreciated.
> >
> > Thanks,
> >
> > Manik Mayur
> > Graduate student
> > Microfluidics Lab
> > Dept. of Mechanical Engg.
> > IIT Kharagpur
> > INDIA
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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> End of gmx-users Digest, Vol 62, Issue 21
> *****************************************
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>
>
>
> --
> "The future belongs to those who believe in the beauty of their dreams."
>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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