[gmx-users] long simulation

Dmitry Kovalsky dikov at imbg.org.ua
Sun May 26 12:18:23 CEST 2002

Hi there,

sorry if a question became trivial but my experience is not too big to 
reply on the question by myself. I've been reading mailing list archive 
concerning PME and RF and steel cann't make decision about mdp parameters to 
chhose for my system. 
I want to simulate my flexible protein that has a charge +4 in water in long 
timescale (near 50 ns). And I want to choose most reasonable parameters for 
my simulation. 

For the correct simulation I have to insert one Na+ ion that binds into the 
structure. So for neutral system it should be 1Na+ and 5 Cl- ions in the 
In order to mimic native-like enviromnent I would like to insert 15 NaCl ion 
pairs more, into my system (if it is correct, please advice me). Finally I 
will compute it on 4CPU cluster (2x2CPU-node). 
The question is that what the PME or the Reaction Field will be reasonable in 
these conditions?

In case of PME my mdp options are:
cpp                 =  /lib/cpp
constraints         = all-bonds
constraint_algorithm =  shake
integrator          =  md
dt                  =  0.001
nsteps              =  50000000
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstfout             =  1000
coulombtype         =  PME
rcoulomb            =  0.9
rcoulomb_switch     =  0
pme_order                = 4
optimize_fft             = yes
fourierspacing      =  0.12
ns_type             =  grid
vdwtype            = Cut-off
rlist                    = 0.9
rvdw                  = 1.5
nstlist                 = 10
ns_type              = grid

Any suggestions are appreceable.

Thanks in advance 

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589

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