Re: [gmx-users] Modified Gromacs and OPENMM

OPENMM? Thanks! Chi-cheng On Fri, Apr 29, 2011 at 3:08 PM, Justin A. Lemkul wrote: > > > Chi-cheng Chiu wrote: > >> Hi Gromacs users & developers, >> If I modified gromacs, will my modification works if I complied it with >> OPENMM and use GPU? >> > &

[gmx-users] Modified Gromacs and OPENMM

Hi Gromacs users & developers, If I modified gromacs, will my modification works if I complied it with OPENMM and use GPU? Thanks! Regards, Chi-cheng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gr

Re: [gmx-users] Still model

uang > > > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Chi-cheng Chiu > *Sent:* Saturday, April 09, 2011 8:33 AM > *To:* gmx-users@gromacs.org > *Subject:* [gmx-users] Still model > > > > Hi all, > > I loo

[gmx-users] Still model

Hi all, I looked at source code in /src/mdlib/genborn.c and have two questions regarding the Still implicit solvent model. 1. in the function calc_gb_chainrule(), only Still model have extra factor of 2 apply on dvda, which I don't know why. 2. in calc_gb_rad_still(), does dccf miss a factor of 2

[gmx-users] implicit solvent GB force table

Hi, I have been tracking the code for implicit solvent, i.e. src/mdlib/genborn.c According to the gromacs paper on implicit solvent, J Comp Chem 31:2593, 2010, the GB force is tabulated in the X = Rij Ci Cj dimension. However, the tabulated function, which I think is stored in fr->gbtab, is only us

[gmx-users] implicit solvent model: formulation of non-polar free energy

Hi everyone, I am going through the source code for the GB calculation part of gromacs, and found the following code in "src/mdlib/genborn.c" : in the function "real calc_gb_nonpolar()" rai = top->atomtypes.gb_radius[md->typeA[ai]]; rbi_inv = fr->invsqrta[ai]; rbi_inv2 = rbi_inv * rbi_in