thank you Justin.Now it is fine.
> ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Jan 2013 22:50:13 +0530 > From: SANTU BISWAS <[email protected]> > Subject: [gmx-users] energy-mimisation-problem > To: [email protected] > Message-ID: > <caewz1z-7yv_8dcaurt+rm6fkdqomcmftxpdkbzl0atyyoor...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > dear users, > > I am performing an energy minimization of > apolypeptide(formed by alanine-10-residues) in vacuum box by using > Steepest Descent(initially) and then Conjugate Gradient methods in > gromacs_4.5.5_doubleprecision.The chain length of > alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range > interactions.so i use cutoff 2.0 nm .But in the > output (.log )file there is a contribution of energy for long-range > interactions(in both energy minimisation methods). > I do not understand why this is happening. > > the input file for energy minimisation is, > > ;title = > cpp = /lib/cpp > ;include =-I../top/ > define = -DFLEXIBLE > ; Input file > integrator = steep/cg > nsteps = 10000 > nstlist = 1 > rlist = 1.0 > rcoulomb = 2.0 > rvdw = 2.0 > ; Energy minimizing stuff > emtol = 0.001 > emstep = 0.1 > nstcgsteep = 10 > > > the output(.log )file is, > > Energies (kJ/mol) > Bond Angle Proper Dih. > Ryckaert-Bell. LJ-14 > 8.48244e+00 2.10205e+01 2.39409e+00 9.86941e+01 > 1.47894e+02 > Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) > Coulomb (LR) > 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 > Potential Pressure (bar) > -1.26841e+03 0.00000e+00 > > ........ > santu > > > ------------------------------ > > Message: 2 > Date: Wed, 09 Jan 2013 12:30:06 -0500 > From: Justin Lemkul <[email protected]> > Subject: Re: [gmx-users] energy-mimisation-problem > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 1/9/13 12:20 PM, SANTU BISWAS wrote: >> dear users, >> >> I am performing an energy minimization of >> apolypeptide(formed by alanine-10-residues) in vacuum box by using >> Steepest Descent(initially) and then Conjugate Gradient methods in >> gromacs_4.5.5_doubleprecision.The chain length of >> alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range >> interactions.so i use cutoff 2.0 nm .But in the >> output (.log )file there is a contribution of energy for long-range >> interactions(in both energy minimisation methods). >> I do not understand why this is happening. >> >> the input file for energy minimisation is, >> >> ;title = >> cpp = /lib/cpp >> ;include =-I../top/ >> define = -DFLEXIBLE >> ; Input file >> integrator = steep/cg >> nsteps = 10000 >> nstlist = 1 >> rlist = 1.0 >> rcoulomb = 2.0 >> rvdw = 2.0 >> ; Energy minimizing stuff >> emtol = 0.001 >> emstep = 0.1 >> nstcgsteep = 10 >> >> > > You haven't set a value for the pbc keyword, so it takes the default value > (xyz). The result is that you're not really minimizing in vacuo, but rather > in > some sort of pseudo-crystal state that probably has lots of periodicity > artifacts. That's probably the source of the energy terms - your peptide > interacting with itself. > > -Justin > >> the output(.log )file is, >> >> Energies (kJ/mol) >> Bond Angle Proper Dih. >> Ryckaert-Bell. LJ-14 >> 8.48244e+00 2.10205e+01 2.39409e+00 9.86941e+01 >> 1.47894e+02 >> Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) >> Coulomb (LR) >> 1.63221e+03 -1.64038e+02 -4.97232e-01 -3.00455e+03 -1.00138e+01 >> Potential Pressure (bar) >> -1.26841e+03 0.00000e+00 >> >> ........ >> santu >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [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
