Indeed. You have to add a parameter rototr = yes. Note that the changes in the .tpr file make it impossible to use these .tpr with other versions of gromacs and vice versa. Besides, you need a reference structure for the removal of the rotation/translation. This file has a fixed name: ref_conf.gro. The best thing to do is to take the .tpr file for the simulation and use editconf with an index file to generate ref_conf.gro from this .tpr (using the desired set of atoms).
If you run into any trouble, please let me know. However, I'm rather busy at this moment, so trouble shooting may take a while.
Good luck,
Tsjerk
On 4/26/06,
Naser, Md Abu <[EMAIL PROTECTED]> wrote:
Hi Tsjerk,Thanks for the link. I have been wondering how to select roto-translation option. Is it in the mdp file?With regards,Abu NaserSchool Of Life SciencesHeriot-Watt UniversityEdinburgh EH14 4ASEmail: [EMAIL PROTECTED]Phone: +44(0)1314518265Fax : +44(0) 131 451 3009
From: Tsjerk Wassenaar
Sent: Wed 26/04/2006 12:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] comm-mode = AngularHi Abu,
In fact, I have it implemented in two versions (3.1.4 and 3.2.1), but haven't contributed it to the official code yet. At this point I don't have the time either :S However, you can download my versions at http://md.chem.rug.nl/~tsjerk/GMX/
Cheers,
Tsjerk
On 4/26/06, Naser, Md Abu <[EMAIL PROTECTED]> wrote:Hi Tsjerk,I have been wondering whether Andrea Amadei and coworkers' method (J. Chem. Phys. 112(1) pp. 9-23) has been implemented in Gromacs yet.With regards,Abu NaserSchool Of Life SciencesHeriot-Watt UniversityEdinburgh EH14 4ASEmail: [EMAIL PROTECTED]Phone: +44(0)1314518265Fax : +44(0) 131 451 3009
From: David van der Spoel
Sent: Tue 25/04/2006 7:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] comm-mode = AngularNaser, Md Abu wrote:
> Hi All,
>
> Dose anyone know any literature regarding comm-mode = Angular option?
it just sets the overall angular momentum to zero.
> With regards,
> Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email:
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>
>
>
> ------------------------------------------------------------------------
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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