Have you checked out the -ndec option for trjconv? If you have a high precision format (.trr, or .xtc if they are stored with sufficient precision) you can print out a .gro file (that gromacs can read) with higher precision.
Gromacs can read .gro files with increased precisions in the coordinates -- as long as the precision does not CHANGE anywhere in the file. On Fri, Jul 5, 2013 at 11:16 AM, C.M.Sampson <cms1...@soton.ac.uk> wrote: > Dear all, > > I use Gromacs 4.5.5 with the AMBER ff99SB force field. > > I'm working on a method that requires me to run short NVE simulations > one after the other, but randomly generating velocities at the start of > each simulation. i.e. I would run 10 ps, use the final structure with > new random velocities and run another 10 ps. > > I had issues with the final potential energy of the previous simulation > not matching the first potential energy of the current simulation, but > managed to fix that by converting the coordinates from the .xtc file to > a .gro file. > > My problem is that when I then put the velocities into my new .gro file > the simulation breaks after the first step and the kinetic energy is way > too high: > > " > Step Time Lambda > 0 0.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 > 5.92468e+03 1.01216e+03 7.68471e-01 6.38163e-01 3.95610e+00 > LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. > 8.66770e+03 -2.27543e+03 5.12418e+04 6.45763e+04 2.11278e+07 > Total Energy Temperature Pressure (bar) > 2.11924e+07 7.81749e+05 1.08075e+07 > " > > The temperature should be 300K and if I use a .gro file with less > decimal places these same velocities work. > > I thought it had to be the way I had formatted my .gro file, but found > the following: > > " > This format is fixed, ie. all columns are in a fixed position. > Optionally (for now only yet with trjconv) you can write gro files with > any number of decimal places, the format will then be n+5 positions with > n decimal places (n+1 for velocities) in stead of 8 with 3 (with 4 for > velocities). Upon reading, the precision will be inferred from the > distance between the decimal points (which will be n+5). Columns contain > the following information (from left to right): > * residue number (5 positions, integer) > * residue name (5 characters) > * atom name (5 characters) > * atom number (5 positions, integer) > * position (in nm, x y z in 3 columns, each 8 positions with 3 > decimal places) > * velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 > positions with 4 decimal places) > " > > within http://manual.gromacs.org/online/gro.html . > > An extract of my .gro file can be seen below: > > " > Generated by trjconv : 2168 system t= 15.00000 > 2168 > 1ETH C1 1 2.735383 2.672010 1.450194 0.2345 -0.1622 > 0.2097 > 1ETH H11 2 0.015804 2.716597 1.460588 0.8528 -0.7984 > 0.6605 > 1ETH H12 3 2.744822 2.565544 1.409227 -2.3812 2.8618 > 1.8101 > " > > I was wondering if there's a way to use a larger number of decimal > places for the coordinates with velocities? > > Best Wishes > > Chris Sampson > > -- > 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
