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<p class="MsoNormal">Hello to everybody<br>
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.<br>
If anybody having any PDF or web link emphasis the analysis part, please
forword me...<br>
Thank you</p>
<br>Rituraj<br><br><div class="gmail_quote">On Wed, Jun 3, 2009 at 9:05 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br>
Today's Topics:<br>
<br>
1. protein running out of box (sheerychen)<br>
2. Re: protein running out of box (Justin A. Lemkul)<br>
3. Re: protein running out of box (ravi sharma)<br>
4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)<br>
5. Some questions regarding generating topologies (Manik Mayur)<br>
6. Re: Some questions regarding generating topologies<br>
(Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 3 Jun 2009 15:37:57 +0200<br>
From: sheerychen <<a href="mailto:sheerychen@gmail.com">sheerychen@gmail.com</a>><br>
Subject: [gmx-users] protein running out of box<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:e1b92dfb0906030637y6cc57951oaf959aafd2b46d30@mail.gmail.com">e1b92dfb0906030637y6cc57951oaf959aafd2b46d30@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello, every body. I have running a MD for 10ns. However, after 5ns part of<br>
protein will running out of the box and be located at other part of the<br>
water box. And the whole structure seems ver strange. It seems that it was<br>
caused by the mass translation but I have used the comm_mode=Linear. Any<br>
suggestions?<br>
<br>
--<br>
Zhen Chen,<br>
Department of Bioprocess and Biosystem Engineering,<br>
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany<br>
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: <a href="mailto:zhen.chen@tuhh.de">zhen.chen@tuhh.de</a><br>
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Message: 2<br>
Date: Wed, 03 Jun 2009 09:46:08 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] protein running out of box<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4A267EA0.8090308@vt.edu">4A267EA0.8090308@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
sheerychen wrote:<br>
> Hello, every body. I have running a MD for 10ns. However, after 5ns part<br>
> of protein will running out of the box and be located at other part of<br>
> the water box. And the whole structure seems ver strange. It seems that<br>
> it was caused by the mass translation but I have used the<br>
> comm_mode=Linear. Any suggestions?<br>
><br>
<br>
What you are seeing is a normal consequence of periodicity. There is no "side"<br>
in an infinite system:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions" target="_blank">http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions</a><br>
<br>
-Justin<br>
<br>
> --<br>
> Zhen Chen,<br>
> Department of Bioprocess and Biosystem Engineering,<br>
> Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany<br>
> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: <a href="mailto:zhen.chen@tuhh.de">zhen.chen@tuhh.de</a><br>
> <mailto:<a href="mailto:zhen.chen@tuhh.de">zhen.chen@tuhh.de</a>><br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
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<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT)<br>
From: ravi sharma <<a href="mailto:rdsharma_4u@yahoo.com">rdsharma_4u@yahoo.com</a>><br>
Subject: Re: [gmx-users] protein running out of box<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:147031.55861.qm@web54606.mail.re2.yahoo.com">147031.55861.qm@web54606.mail.re2.yahoo.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Zhen Chen<br>
<br>
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.<br>
<br>
<br>
regards<br>
<br>
Ravi Datta Sharma Lecturer, Bioinformatics,<br>
Department of Microbiology,<br>
CCS Unversity,<br>
Meerut<br>
<br>
<br>
<br>
--- On Wed, 3/6/09, sheerychen <<a href="mailto:sheerychen@gmail.com">sheerychen@gmail.com</a>> wrote:<br>
<br>
From: sheerychen <<a href="mailto:sheerychen@gmail.com">sheerychen@gmail.com</a>><br>
Subject: [gmx-users] protein running out of box<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Date: Wednesday, 3 June, 2009, 7:07 PM<br>
<br>
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?<br>
<br>
<br>
--<br>
Zhen Chen,<br>
Department of Bioprocess and Biosystem Engineering,<br>
Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany<br>
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: <a href="mailto:zhen.chen@tuhh.de">zhen.chen@tuhh.de</a><br>
<br>
<br>
<br>
-----Inline Attachment Follows-----<br>
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Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
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<br>
Message: 4<br>
Date: Wed, 3 Jun 2009 14:43:09 +0000<br>
From: Rebeca Garc?a Fandi?o <<a href="mailto:regafan@hotmail.com">regafan@hotmail.com</a>><br>
Subject: [gmx-users] spc.itp for the amber force field<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BAY142-W27797B710E741D553D80E4B74A0@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hi,<br>
<br>
I am trying to simulate a system using the parameters for ions developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce).<br>
<br>
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.<br>
<br>
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?<br>
<br>
Thank you very much for your help.<br>
<br>
Best wishes,<br>
<br>
<br>
<br>
Rebeca Garcia<br>
<br>
Academic Visitor<br>
<br>
Oxford University<br>
<br>
_________________________________________________________________<br>
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<br>
Message: 5<br>
Date: Wed, 3 Jun 2009 20:57:57 +0530<br>
From: Manik Mayur <<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.com</a>><br>
Subject: [gmx-users] Some questions regarding generating topologies<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:7e56bc410906030827t5c183f2fxb10049788c1b1c85@mail.gmail.com">7e56bc410906030827t5c183f2fxb10049788c1b1c85@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
Even though after going through the manual, I still have some basic<br>
confusions regarding generating topologies.<br>
<br>
1) I have generated an itp file after adding some Cl- ions using genion. It<br>
goes like this:<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
Cl_ion 0<br>
<br>
[ atoms ]<br>
; nr type resnr residue atom cgnr charge mass<br>
typeB chargeB massB<br>
1 CL- 1 Cl- Cl 1 -1 35.453 ; qtot<br>
-1<br>
2 CL- 2 Cl- Cl 2 -1 35.453 ; qtot<br>
-2<br>
3 CL- 3 Cl- Cl 3 -1 35.453 ; qtot<br>
-3<br>
........<br>
........<br>
<br>
To allow nb interactions between all the atoms in the molecule Cl_ion, is<br>
setting nrexcl = 0 okay?<br>
<br>
2) In spce.itp provided with GROMACS,<br>
<br>
[ moleculetype ]<br>
; molname nrexcl<br>
SOL 2<br>
<br>
while in the manual, on pg. 100 (Chapter-5 Topologies)<br>
[ moleculetype ]<br>
; molname nrexcl<br>
SOL 1<br>
<br>
why is the inconsistency?<br>
<br>
3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended).<br>
Since SPC/E is one of the most used model, should I consider using OPLS<br>
rather than GROMOS96, otherwise how significant will be the errors?<br>
<br>
4) I am using GROMOS96 43a1, so am I allowed to change combination rule to<br>
'2' ( '1' is the default). How significantly will it affect the<br>
simulations?<br>
<br>
Any relevant idea/suggestion/reference is appreciated.<br>
<br>
Thanks,<br>
<br>
Manik Mayur<br>
Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
INDIA<br>
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------------------------------<br>
<br>
Message: 6<br>
Date: Wed, 03 Jun 2009 11:34:34 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Some questions regarding generating<br>
topologies<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4A26980A.1000205@vt.edu">4A26980A.1000205@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Manik Mayur wrote:<br>
> Hi,<br>
><br>
> Even though after going through the manual, I still have some basic<br>
> confusions regarding generating topologies.<br>
><br>
> 1) I have generated an itp file after adding some Cl- ions using genion.<br>
> It goes like this:<br>
><br>
<br>
This is unnecessary. Just #include "ions.itp" and the parameters for Cl- for<br>
whatever force field you're using are included.<br>
<br>
> [ moleculetype ]<br>
> ; Name nrexcl<br>
> Cl_ion 0<br>
><br>
> [ atoms ]<br>
> ; nr type resnr residue atom cgnr charge mass<br>
> typeB chargeB massB<br>
> 1 CL- 1 Cl- Cl 1 -1 35.453 ;<br>
> qtot -1<br>
> 2 CL- 2 Cl- Cl 2 -1 35.453 ;<br>
> qtot -2<br>
> 3 CL- 3 Cl- Cl 3 -1 35.453 ;<br>
> qtot -3<br>
> ........<br>
> ........<br>
><br>
> To allow nb interactions between all the atoms in the molecule Cl_ion,<br>
> is setting nrexcl = 0 okay?<br>
><br>
> 2) In spce.itp provided with GROMACS,<br>
><br>
> [ moleculetype ]<br>
> ; molname nrexcl<br>
> SOL 2<br>
><br>
> while in the manual, on pg. 100 (Chapter-5 Topologies)<br>
> [ moleculetype ]<br>
> ; molname nrexcl<br>
> SOL 1<br>
><br>
> why is the inconsistency?<br>
><br>
<br>
Probably just a typo.<br>
<br>
> 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is<br>
> recommended). Since SPC/E is one of the most used model, should I<br>
> consider using OPLS rather than GROMOS96, otherwise how significant will<br>
> be the errors?<br>
><br>
<br>
An excellent comparison of different force fields and different water models can<br>
be found in:<br>
<br>
Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.<br>
<br>
> 4) I am using GROMOS96 43a1, so am I allowed to change combination rule<br>
> to '2' ( '1' is the default). How significantly will it affect the<br>
> simulations?<br>
><br>
<br>
I would say it invalidates everything. The defaults for combination rules,<br>
bonded parameters, etc. are as much a part of each force field as the atom types<br>
and charges.<br>
<br>
-Justin<br>
<br>
> Any relevant idea/suggestion/reference is appreciated.<br>
><br>
> Thanks,<br>
><br>
> Manik Mayur<br>
> Graduate student<br>
> Microfluidics Lab<br>
> Dept. of Mechanical Engg.<br>
> IIT Kharagpur<br>
> INDIA<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
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*****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>"The future belongs to those who believe in the beauty of their dreams."<br>