Hi all, I have 2 questions related to the electrostatic energy of the system..
1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*. OR *Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused. I specified in my .mdp file; coulombtype = PME rvdw = 1.0 rlist = 1.0 rcoulomb = 1.0 fourierspacing = 0.16 pme_order = 4 ewald_rtol = 1e-5 2) I want to calculate electrostatic interaction energy between 2 residues in my system which has 10 peptides in total. But I think, I should have specified the energy groups composed of that 2 residues in my mdp file before starting the simulation. So in this case, is there any way to get this interaction energy OR can I just calculate the electrostatic energy of the whole system? Thanks in advance, Turgay 2012/6/8 Mark Abraham <[email protected]> > On 8/06/2012 11:51 PM, Turgay Cakmak wrote: > > Thanks Mark. > I want to calculate Coulomb and Lennard-Jones energies using > total_dt100.edr . > But, I am not sure I can get the correct energies? > > > Neither am I. Only you know the history of these .edr files. > > Mark > > > > Turgay > > 2012/6/8 Mark Abraham <[email protected]> > >> On 8/06/2012 10:40 PM, Turgay Cakmak wrote: >> >> >> Hi all, >> >> I have encountered a problem using eneconv with -dt flag. >> I have several energy files. Firstly, I concatenated them using the >> following. >> >> eneconv -f first.edr second.edr .... -settime -o total.edr >> >> But, total.edr is so large. To reduce the size of file, I used the below >> command: >> >> eneconv -f total.edr -dt 100 -o total_dt100.edr >> >> But, I get the following warning: >> * .* >> * .* >> >> WARNING: missing energy sums at time 69984.000000 >> >> WARNING: missing energy sums at time 69988.000000 >> >> WARNING: missing energy sums at time 69992.000000 >> >> WARNING: missing energy sums at time 69996.000000 >> Reading energy frame 35000 time 70000.000 >> WARNING: missing energy sums at time 70000.000000 >> Last energy frame read 35000 time 70000.000 >> Last step written from energy.edr: t 70000, step 35000000 >> >> Last frame written was at step at step 35000000, time 70000.000000 >> Wrote 701 frames >> >> >> At some point something did something to break the usual format of the >> files... but we can have no idea what. >> >> >> >> Eventually, I get the "total_dt100.edr". But, I am not sure I could >> continue using this file. >> If someone could help me, I would be glad. >> >> >> Depends what you want to use it for. >> > > >> >> Mark >> >> -- >> 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 >> > > > > > > -- > 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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