Thank you Mark for your response. I only need to double check a few things for which using generic C kernels should suffice. I need to run only 1 or 2 steps and not in parallel. Thanks again for your help. Sapna
On Wed, Sep 15, 2010 at 9:43 PM, Mark Abraham <[email protected]>wrote: > > > ----- Original Message ----- > From: sapna sarupria <[email protected]> > Date: Thursday, September 16, 2010 1:35 > Subject: [gmx-users] Wrtiing pair interaction energy on the fly > To: Discussion list for GROMACS users <[email protected]> > > > Dear all > > > > I understand that pair interactions in gromacs are calculated through > assembly loops. Can some one guide me to the resources using which I can > write out the interaction energy/force for each pair directly from gromacs > during the simulation (without using the rerun option). The rerun option is > especially difficult when you want pair interaction between all atoms of > one's system since one has to define that many index groups. I most cases > rerun is good, but in my case I have to test interaction between several > pairs. > > You are limited to 256 energy groups with or without using -rerun. If you > need more, then perhaps you should consider some other simulation software > that is better suited to this task. With GROMACS, you could use an > environment variable to force the use of the generic C kernels, and inside > that kernel use printf to write out the energy for each interaction. This > will be horribly slow, and will be vastly simpler if not attempted in > parallel. > > Mark > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream
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