[gmx-users] h-bonds constraints for DPPC sim?

Hi It was mentioned here http://lists.gromacs.org/pipermail/gmx-users/2011-May/061475.html that the constraints option may have to be set to h-bonds to get the exp APL in DPPC equilibration/simulation. Is this indeed true and if so how important is it for membrane/protein simulations? Thanks in

[gmx-users] h-bonds constraints

Hi I want to run an NPT simulation with all h-bonds constrained. How does grompp identify the Hydrogen atoms given that forcefield labels like HA, HC, HE are used. Is it the mass? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] h-bonds constraints

Thanks! That's reasonable. On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu wrote: > On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban > wrote: >> What criterion does the grompp utility use to identify H-atoms when it >> is requested in the MDP file to apply constraints=h-bonds? Thanks. > >

Re: [gmx-users] h-bonds constraints

On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban wrote: > What criterion does the grompp utility use to identify H-atoms when it > is requested in the MDP file to apply constraints=h-bonds? Thanks. Any atom name starting with H or h (so case-insensitive). Cheers, Bogdan -- gmx-users mailing

[gmx-users] h-bonds constraints

What criterion does the grompp utility use to identify H-atoms when it is requested in the MDP file to apply constraints=h-bonds? Thanks. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing lis