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On 22/11/2011 10:08 PM, ifat shub wrote:
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<div>Hi,</div>
<div>I am running simulations using implicit solvent. I am using
the pbc = no option in my mdp file, however, I see it the .gro
file that gromacs is creating a box for the system.What is the
effect of the box in implicit solvent simulations?</div>
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<br>
None, if pbc = no. When writing a .gro file some data has to go into
the space the format allows for the box. However the .mdp file
controls whether that is significant. Later on when using analysis
tools, some of the analyses might erroneously use that box if you
don't give suitable instructions not to.<br>
<br>
Mark<br>
<br>
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<div> </div>
<div>This is the mdp file that I am using:</div>
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<p>------run.mdp------</p>
<p>integrator = md</p>
<p>nsteps = 20000</p>
<p>dt = 0.001</p>
<p>implicit_solvent = GBSA</p>
<p>pbc = no</p>
<p>nstlist = 0</p>
<p>ns_type = simple</p>
<p>rlist = 0</p>
<p>rgbradii = 0</p>
<p>coulombtype = Cut-off</p>
<p>rcoulomb = 0</p>
<p>vdwtype = Cut-off</p>
<p>rvdw = 0</p>
<p>tcoupl = v-rescale</p>
<p>tc_grps = system</p>
<p>tau_t = 0.1 </p>
<p>ref_t = 1000</p>
<p>energygrps = Protein_chain_A Protein_chain_C
Protein_chain_E Protein_chain_G Protein_chain_I
Protein_chain_K</p>
<p>gen_vel = yes</p>
<p>gen_temp = 1000</p>
<p>ld_seed = -1</p>
<p>gen_seed = -1</p>
<p>nstxout = 1</p>
<p>nstvout = 1</p>
<p>nstxtcout = 1</p>
<p>nstenergy = 1</p>
<p>------------------</p>
</span></div>
<div>Thanks,</div>
<div>Ifat</div>
<div> </div>
<div>M.Sc. Student<br>
Bar Ilan University<br>
Ramat Gan<br>
Israel<br>
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