Hey Mark Do you mean removing all bond definitions from topology file, when you say well constructed topology to exclude all bonded-interactions in rerun?
thanks sikandar On Sat, May 14, 2011 at 8:01 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 14/05/2011 10:52 PM, XAvier Periole wrote: > >> >> Two things you have to be careful about: >> 1- use trr trajectory files. xtc precision is not sufficient and it will >> give a lot of discrepancies at least for the bonded terms. >> 2- set the nstlist to 1 as the neiboring list should be undated for each >> frame and not every 5/10 as it is normally set in a regular mdp file. >> > > Reruns do neighbour searching every frame, regardless. > > Mark > > > >> On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote: >> >> >>> >>> Ramachandran G wrote: >>> >>>> Hello gmx users: >>>> I did 1ns simulation for my system and have the trajectory and >>>> energy files. >>>> Now i want to see the energy of some specific residues. So, i >>>> decompose(separated) the energy groups and edited the mdp file. >>>> Using the mdp file, i created a new tpr file and rerun the mdrun using >>>> the trajectory file. But when i compared the total energy between the old >>>> and new one, it differs a lot. >>>> I am doing some mistakes somewhere. Can anyone help me please. Thanks. >>>> >>> >>> Maybe, maybe not. Without seeing the .mdp settings and the data that >>> you're looking at, all anyone can do is guess. You also haven't stated what >>> type of trajectory (i.e. .xtc or .trr) you're using as -rerun input. If >>> you're using an .xtc file, there is no velocity information, so any property >>> related to velocities (most notably kinetic energy, but several others as >>> well) will be zero. I suspect this is probably where the discrepancy is, >>> but it is not a problem. Using energygrps is only useful for decomposing >>> short-range nonbonded energy terms, nothing else. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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