Hi, Thanks.
Ok so some more info: I am developing a coarse-grained model of peptides based on an elastic network approach. Rather than run the simulations in vacuum I wanted to use Langevin dynamics to dampen the motions. Also, at the moment if I simulate very long, thin polymers I get big fluctuations in my energies (have tried NVT, NPT and NVE). I have tried to reduce the time step, but this does not solve the energy problem. So the simulation starts off ok- the energy is fine- but after a time, the ends of my polymer start to 'waggle' a lot and this is when the energy begins to drift. I thought using Langevin dynamics might prevent this. Any ideas would gratefully received, -Syma -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess Sent: 04 July 2006 13:50 To: [email protected] Subject: RE: [gmx-users] Langevin dynamics >From: "syma" <[EMAIL PROTECTED]> >Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users ><[email protected]> >To: "'Discussion list for GROMACS users'" <[email protected]> >Subject: [gmx-users] Langevin dynamics >Date: Tue, 4 Jul 2006 11:06:35 +0100 > >Hi, > >I am still trying to do Langevin dynamics in gromacs- does anyone know >(ball >park) what would be reasonable values to use for the frictional term when >simulating helical peptides in solution? You did not give enough information. Are you using explicit or implicit solvent? With implicit solvent you can use Stokes law to estimate the value. But Gromacs does not come with an implicit solvent force field. Any explicit solvent force field will give completely wrong results if you just leave out the solvent. Berk. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
