[gmx-users] Simulation Questions

[James R. Graham]

Hello All,

I am new to gromacs (and am coming at this from a background not  
fully steeped in molecular dynamics), so please excuse any naive  
questions.

Basically, I am trying to predict possible structures a chemically- 
synthesized peptide may adopt in solution.

I create a sequence-based PDB file of a peptide (anywhere from 10 to  
~30 in length) in PyMOL, then bring that over to gromacs (using the  
GROMOS96 43a2 forcefield), solvate it, and run a minimization (1  
nanosecond MD run of the peptide in a box of water, see appended .mdp  
file below).

The current simulation (of a 15-mer) gets to step 186 (time 0.372  
(ps)) and just seems to hang there.

Are there different parameters that I should be using for this type  
of sim? I am most interested in overall, gross structure rather than  
something very finely tuned.

With the waters, there are a total of 2598 atoms (I had to set the  
box size to 3).

Any advice would be greatly appreciated.

Cheers,
james

mdp file:
title                    = whatever
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 500000
nstxout                  = 5000
nstvout                  = 5000
nstlog                   = 5000
nstenergy                = 250
nstxtcout                = 250
xtc_grps                 = Protein
energygrps               = Protein  SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.8
coulombtype              = cut-off
rcoulomb                 = 1.4
rvdw                     = 0.8
tcoupl                   = yes
tc-grps                  = Protein      SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
solvent_optimization     = SOL
constraints              = all-bonds