[gmx-users] Issues with NEMD simulations

[shikha nangia]

Dear all,



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).



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.



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?



Here is the full mdp file for the NEMD run:

title                    = Martini

cpp                      = 
/usr/bin/cpp

integrator               = md

tinit                   
 = 0.0

dt                       = 0.01

nsteps                   =
 500

nstcomm                  = 1

comm-grps                        
 = system

nstxout                  = 10

nstvout                  =
 10

nstfout                  = 10

nstlog                   = 10

nstenergy               
 =
 10

nstxtcout                = 2500

xtc_precision            = 100

xtc-grps                
 = 

energygrps               = system

nstlist                  = 1

ns_type                 
 = grid

pbc                      = xyz

rlist                    =
 1.7

coulombtype              = Shift 

rcoulomb_switch          = 
0.0

rcoulomb                 = 1.2

epsilon_r                = 15

vdw_type                
 = Shift 

rvdw_switch              = 0.9

rvdw                     =
 1.2

DispCorr                 =
 EnerPres

tcoupl                   = V-rescale

tc-grps                 
 = NGL W

tau_t                    = 1.0 1.0 

ref_t                   
 = 300. 300.

Pcoupl                   = No

Pcoupltype              
 = Isotropic

tau_p                    = 1.0 

compressibility         
 =
 1e-5

ref_p                    = 1.0 

gen_vel                  = 
Yes

gen_temp                 = 300

gen_seed                 = 
473529

constraints              = None

constraint_algorithm     = Lincs

unconstrained_start     
 = no

lincs_order              = 1

lincs_warnangle          = 30



;
 Non-equilibrium MD
 stuff

acc-grps                 =  NGL W

accelerate               
=  0.1 0 0 -0.1 0 0

freezegrps               =   

freezedim               
 =   

cos_acceleration         = 0.1 

deform                   =  



Best,

SN
Dr. Shikha Nangia
201D Chemistry Building  Department of Chemistry 
The Pennsylvania State University  University Park, PA 16802  
Phone(o): 814-863-0289
Phone(cell): 612-599-9449 
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