Dear Mark, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane with dual topology.
topology A (lambda=0) to topology B (lambda=1) What i obtained after using mdrun command to calculate free energy is dgdl.xvg that contain dV(total)/dlamda via time. I want to obtein dV(bond)/dlamda and dV(non-bond)/dlamda, seperetly. dV(bond)/dlambda and dV(non-bond)/dlambda are not writed in free.edr and free.log. how to produce dv(bond)/dlambda and dV(non-bond)/dlambda. my version gromacs is 4.0.5 and 4.0.7. Thanks in advance, Maleki On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <[email protected]>wrote: > On 9/08/2011 9:13 PM, afsaneh maleki wrote: > > Hi, > > > > I used thermodynamics integration method (TI) to obtain delta Gibbs energy > of the protein membrane. I want to separate contributions of delta bonding > and nonbonding energy in delta Gibbs energy. > > > So instead of using the sum of bonded and non-bonded energy (i.e. total > PE), use them separately. Whether that will mean anything is up to you to > demonstrate. > > Mark > > > > Best wishes, > > Maleki, > > > > > -- > 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 >
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