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... Thank you
Rituraj On Wed, Jun 3, 2009 at 9:05 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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 <[email protected]> > Subject: [gmx-users] protein running out of box > To: [email protected] > Message-ID: > <[email protected]> > 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: [email protected] > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/20c8cd2e/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 03 Jun 2009 09:46:08 -0400 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] protein running out of box > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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: [email protected] > > <mailto:[email protected]> > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 [email protected]. > > 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 | (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 <[email protected]> > Subject: Re: [gmx-users] protein running out of box > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> wrote: > > From: sheerychen <[email protected]> > Subject: [gmx-users] protein running out of box > To: [email protected] > 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: [email protected] > > > > -----Inline Attachment Follows----- > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > Own a website.Get an unlimited package.Pay next to nothing.*Go to > http://in.business.yahoo.com/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/d6648143/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Wed, 3 Jun 2009 14:43:09 +0000 > From: Rebeca Garc?a Fandi?o <[email protected]> > Subject: [gmx-users] spc.itp for the amber force field > To: <[email protected]> > Message-ID: <[email protected]> > 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 > > _________________________________________________________________ > Chatea sin límites en Messenger con la tarifa plana de Orange > http://serviciosmoviles.es.msn.com/messenger/orange.aspx > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/1257dcc7/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 3 Jun 2009 20:57:57 +0530 > From: Manik Mayur <[email protected]> > Subject: [gmx-users] Some questions regarding generating topologies > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/7be6fcde/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Wed, 03 Jun 2009 11:34:34 -0400 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Some questions regarding generating > topologies > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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 [email protected] > > 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 [email protected]. > > 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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 62, Issue 21 > ***************************************** > -- "The future belongs to those who believe in the beauty of their dreams."
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