So cite the error please. I did not find the error regarding degrees of freedom below.
Do you want to keep your PE in vacuum? Dr. Vitaly Chaban > The actual box I got by replicating monomer units has size of 15 0.5 0.5!!!! > That is chain has no space to move. I know you have already given me some > tips on high repulsion in the system but that had to do with incorrect > topology file. I assure you I have learned a lot from your tips ;) > This time I need to have such packed system because that gives me the > density I want. 0.9g/cm3 for PE! for a chain of 60 ethylene units the size > should be identical to the actual size 15 0.5 0.5. And I am wondering how > can I work with much longer chains ( 20 times longer)... > > md grompp is giving error about degrees of freedom. Any advise on this in > appreciated... > > Thank you, > > md > grompp**************************************************************************** > aking dummy/rest group for Acceleration containing 2896 elements > Making dummy/rest group for Freeze containing 2896 elements > Making dummy/rest group for Energy Mon. containing 2896 elements > Making dummy/rest group for VCM containing 2896 elements > Number of degrees of freedom in T-Coupling group Eth is 5373.22 > Number of degrees of freedom in T-Coupling group EthB is 211.89 > Number of degrees of freedom in T-Coupling group EthE is 211.89 > Making dummy/rest group for User1 containing 2896 elements > Making dummy/rest group for User2 containing 2896 elements > Making dummy/rest group for XTC containing 2896 elements > Making dummy/rest group for Or. Res. Fit containing 2896 elements > Making dummy/rest group for QMMM containing 2896 elements > T-Coupling has 3 element(s): Eth EthB EthE > Energy Mon. has 1 element(s): rest > Acceleration has 1 element(s): rest > Freeze has 1 element(s): rest > User1 has 1 element(s): rest > User2 has 1 element(s): rest > VCM has 1 element(s): rest > XTC has 1 element(s): rest > Or. Res. Fit has 1 element(s): rest > QMMM has 1 element(s): rest > > mdpfile************************************************************************************** > > title = PE-Hexane > ;define = -DPOSRES ; tells gromacs to perform position > restrained dynamics/include posre.itp into topology used for position > restraint > pbc = xyz ; use priodic BCs in all > directions > > ; Run control > integrator = md ; type of dynamics algorithm. Here > md uses a leap-frog algorithm for integrating Newtons's eq of motion > dt = 0.002 ; in ps ! > nsteps = 5000 ; length of simulation= nsteps*dt > nstcomm = 1 ; frequency for center of mass > motion removal > > ; Output control > nstenergy = 100 ; frequency to write energies to > energy file. i.e., energies and other statistical data are stored every 10 > steps > nstxout = 100 ; frequency to write > coordinates/velocity/force to output trajectory file. how often snapshots > are collected= nstxout*dt > nstvout = 100 > nstfout = 0 > nstlog = 100 ; frequency to write energies to log > file > nstxtcout = 10 ; frequency to write coordinates to > xtc trajectory > > ; Neighbor searching > nstlist = 10 ; frequency to update neighbor list. > Neighborlist will be updated at least every 10 steps. Manual p80 > ns_type = grid ; make a grid in the box and only > check atoms in neighboring grid cells when constructing a new neighbor list > every nstlist steps > > ; Electrostatics/VdW > coulombtype = Shift ; tells gromacs how to model > electrostatics. Coulomb/LJ potential is decreased over the whole range and > forces decay smoothly to zero betw$ > vdw-type = Shift ; rcoulomb-switch/rvw-switch & > rcoulomb/rvdw > rcoulomb-switch = 0 ; where to start switching the > Coulomb potential > rvw-switch = 0 ; where to start switching the LJ > potential > > ; Cut-offs > rlist = 1.1 ; in nm. Cut-off distance for > short-range neighbor list > rcoulomb = 1.0 ; distance for coulomb cut-off > rvdw = 1.0 ; distance for coulomb cut-off > > ; Temperature coupling > Tcoupl = berendsen > tc-grps = Eth EthB EthE ;HEX ; groups to couple > to thermostat; Berendsen temperature coupling is on in these groups > tau_t = 0.1 0.1 0.1 ;0.1 ; time constant for > T coupling > ref_t = 300 300 300 ;300 ; reference T for > coupling. When you alter the T, don't forget to change the gen_temp for > velocity generation > > ; Pressure coupling > Pcoupl = berendsen ; Pressure coupling is not on > Pcoupltype = isotropic ; means the box expands and > contracts in all directions (x,y,z) in order to maintain the proper pressure > tau_p = 0.5 ; time constant for coupling in ps > compressibility = 4.5e-5 ; compressibility of solvent used in > simulation in 1/bar > ref_p = 1.0 ; reference P for coupling in bar > > ; Velocity generation Generate velocites is on at 300 K. > Manual p155 > gen_vel = yes ; generate velocites according to > Maxwell distribution at T: gen_temp with random gen seed gen_seed > gen_temp = 300.0 ; T for Maxwell distribution > gen_seed = 173529 ; used to initialize random > generator for random velocities > > ; Bonds > constraints = all-bonds ; sets the LINCS constraint for all > bonds > constraint-algorithm = lincs > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100712/21962bb6/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 75, Issue 70 > ***************************************** > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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