<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear all,<br>
<br>
1. I am performing MD simulation of a MARTINI coarse grained polymeric
chains (named NGL in my mdp file below) in Coarse grained water (named W
in mdp file below).<br>
<br>
2. My equilibration and MD runs have been running perfectly until now.
I have started doing NEMD simulations to get viscosity. The starting
structure for NEMD came from an equilibrated system.<br>
<br>
3. I am pretty sure that the error is in the mdp file. I am new to NEMD
so it will be great if I can get some pointers of solving the issue. Is
there a NEMD gromacs tutorial on the web?<br>
<br>
Here is the full mdp file for the NEMD run:<br>
title = Martini<br>
cpp =
/usr/bin/cpp<br>
integrator = md<br>
tinit
= 0.0<br>
dt = 0.01<br>
nsteps =
500<br>
nstcomm = 1<br>
comm-grps
= system<br>
nstxout = 10<br>
nstvout =
10<br>
nstfout = 10<br>
nstlog = 10<br>
nstenergy
=
10<br>
nstxtcout = 2500<br>
xtc_precision = 100<br>
xtc-grps
= <br>
energygrps = system<br>
nstlist = 1<br>
ns_type
= grid<br>
pbc = xyz<br>
rlist =
1.7<br>
coulombtype = Shift <br>
rcoulomb_switch =
0.0<br>
rcoulomb = 1.2<br>
epsilon_r = 15<br>
vdw_type
= Shift <br>
rvdw_switch = 0.9<br>
rvdw =
1.2<br>
DispCorr =
EnerPres<br>
tcoupl = V-rescale<br>
tc-grps
= NGL W<br>
tau_t = 1.0 1.0 <br>
ref_t
= 300. 300.<br>
Pcoupl = No<br>
Pcoupltype
= Isotropic<br>
tau_p = 1.0 <br>
compressibility
=
1e-5<br>
ref_p = 1.0 <br>
gen_vel =
Yes<br>
gen_temp = 300<br>
gen_seed =
473529<br>
constraints = None<br>
constraint_algorithm = <span class="yshortcuts" id="lw_1302986270_1">Lincs</span><br>
unconstrained_start
= no<br>
lincs_order = 1<br>
lincs_warnangle = 30<br>
<br>
;
Non-equilibrium MD
stuff<br>
acc-grps = NGL W<br>
accelerate
= 0.1 0 0 -0.1 0 0<br>
freezegrps = <br>
freezedim
= <br>
cos_acceleration = 0.1 <br>
deform = <br>
<br>
Best,<br>
SN<br><div><font style="background-color: rgb(255, 255, 255);" color="#0000ff">Dr. Shikha Nangia<br>201D Chemistry Building</font></div> <div><font style="background-color: rgb(255, 255, 255);" color="#0000ff">Department of Chemistry <br>The Pennsylvania State University</font></div> <div><font style="background-color: rgb(255, 255, 255);" color="#0000ff">University Park, PA 16802 <br></font><font style="background-color: rgb(255, 255, 255);" color="#0000ff">Phone(o): 814-863-0289<br>Phone(cell): 612-599-9449</font><font color="#ff0000"> <br></font></div><font color="#ff0000"></font></td></tr></table>