[gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 20 15:01:34 CEST 2011

On 20/10/2011 7:25 PM, Vedat Durmaz wrote:
> thanks mark. i guess it took some time answering all these questions. 
> and i think you are right. trying to interpret each computed energy 
> term seperately in a physical manner is senseless. especially since 
> i'm not really deep inside the force field & implementation stuff. 
> however, with one of your statements i cannot agree at all:
> imho, free energy diff's on the basis of two conformations and their 
> steady state distribution are independent from both the energy and 
> type of the intermediate state. it's only the conversion's rate that 
> does depend on it.

I'm not sure with which statement of mine you are disagreeing. The free 
energy is a state function, and so the free energy difference between E 
and Z isomers does not depend on the path taken for the conversion. The 
difficulty is just that there is no path for a cyclic alkane from E to Z 
in a normal MD force field.

> but the reason, why i refrained from extracting the potential energy 
> for a subset of my system was simply due to the difficulties to find 
> "detailed information" about how to play it out although many gromacs 
> users have been asking for the issue over the last years. i needed 
> nearly one full day to figure it out even though it's a simple series 
> of about 4 gromacs commands only, given some md input & result files 
> like md.xtc, md.gro, complex.top, index.ndx:
> |grompp -f mdSubset.mdp -c md.gro -p complex.top -o mdSubsetTemp.tpr|
> |echo ||"1"| || tpbconv -s mdSubsetTemp.tpr -nsteps ||0| |-n index.ndx 
> -o mdSubset.tpr|
> |echo ||"1"| || trjconv -s mdSubset.tpr -f md.xtc -o mdSubset.xtc|
> |mdrun -s mdSubset.tpr -rerun mdSubset.xtc -v -deffnm mdSubset|
> where "1" stands for the group to be extracted (from the list of 
> groups in the index file) and "-nsteps 0" causes recomputation of for 
> the extracted subset at the given time steps only. i mention it here 
> so that other users looking for the details might find them a little 
> bit faster ... it's especially this kind of "tiny tutorials" that i 
> miss e. g. on the gromacs website.

There's an art to trying to find detailed help. I know I've given the 
advice to make subsets and use mdrun -rerun several times, but I don't 
know how a newcomer is ever going to figure that out on their own!

BTW -nsteps 0 is not necessary. mdrun -rerun only computes on the frames 
present in the input trajectory file. Also, if the index group of 
interest is already present in the .tpr that ran the simulation, then 
you can do the job with variations on only the latter three commands.


> thanks for listening and kind regards,
> vedat
>>> Q8 does anyone have an idea, how to perform the simulation and on 
>>> which energy terms to concentrate in order to get reliable results?
>> You seem to be performing it OK, given that you've said very little 
>> about any details...
>> I think the problem is poorly constructed. You have some experimental 
>> data that gives a general understanding of the size of the free 
>> energy difference between the isomers. You can't necessarily expect 
>> to reproduce that from (average) potential energy differences between 
>> conformations of those isomers. Measuring the free energy difference 
>> with simulations is hard because you cannot model the intermediate 
>> stages of bond breaking and forming. There are "alchemical" free 
>> energy methods that could in principle treat this problem 
>> effectively, but there will be some significant issues and you are 
>> best doing your own homework there.
>> Mark

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111021/a5dba6d0/attachment.html>

More information about the gromacs.org_gmx-users mailing list