Dear Gromacs Users,<br><br>I have a protein lipid bilayer system built
using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the
built in system using NPT ensemble, for that i have made to mdp files
and as i have never used Charmm, I am not sure whether the mdp files i
am using are correct, so I want to know your any suggestions and
corrections in my mdp files (below), so that i can use the corrected mdp
file to simulate the system. <br>
<br><b>1st mdp file :</b><br><br>title = Bilayer-500
<br>cpp = /lib/cpp
<br>constraints = all-bonds
<br>integrator = md; A leap-frog algorithm for integrating Newton's equations of motion
<br>dt = 0.002
<br>tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd)
<br>nsteps = 2000000 ; 4 ns
<br>nstcomm = 1
<br>nstxout = 5000
<br>nstvout = 5000
<br>nstfout = 0
<br>nstxtcout = 500
<br>xtc_precision = 1000
<br>nstlog = 500
<br>nstenergy = 500
<br>nstlist = 10
<br>; long range interactions
<br>coulombtype = PME
<br>rlist = 1.2; neighborlist cut-off
<br>rcoulomb = 1.2; Coulomb cut-off
<br>rvdw = 1.2; VdW cut-off
<br>fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME
<br>pme_order = 4
<br>; Berendsen temperature coupling is on in two groups
<br>Tcoupl = berendsen
<br>tau_t = 0.1 0.1 0.1
<br>tc-grps = protein POP SOL
<br>ref_t = 303 303 303
<br>; Energy monitoring
<br>energygrps = protein POP SOL
<br>; pressure coupling is on
<br>Pcoupl = berendsen
<br>pcoupltype = semiisotropic
<br>tau_p = 1.0 1.0
<br>compressibility = 4.5e-5 4.5e-5
<br>ref_p = 1.0 1.0
<br><br>gen_vel = yes
<br>gen_temp = 303.0
<br>gen_seed = 478905<br><br>2nd mdp file:<br>title = Bilayer-500
<br>cpp = /lib/cpp
<br>constraints = all-bonds
<br>integrator = md; A leap-frog algorithm for integrating Newton's equations of motion
<br>dt = 0.002
<br>tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd)
<br>nsteps = 2000000 ; 4 ns
<br>nstcomm = 1
<br>nstxout = 5000
<br>nstvout = 5000
<br>nstfout = 0
<br>nstxtcout = 500
<br>xtc_precision = 1000
<br>nstlog = 500
<br>nstenergy = 500
<br>nstlist = 10
<br>; long range interactions
<br>rlist = 1.2
<br>rlistlong = 1.4
<br>rcoulomb = 1.2
<br>rvdw = 1.0
<br>vdwtype = switch
<br>rvdw_switch = 0.8
<br>coulombtype = PME
<br>pme_order = 4
<br>fourierspacing = 0.16
<br> <br>; Berendsen temperature coupling is on in two groups
<br>Tcoupl = berendsen
<br>tau_t = 0.1 0.1 0.1
<br>tc-grps = protein POP SOL
<br>ref_t = 303 303 303
<br>; Energy monitoring
<br>energygrps = protein POP SOL<br>; pressure coupling is on
<br>Pcoupl = berendsen
<br>pcoupltype = semiisotropic
<br>tau_p = 1.0 1.0
<br>compressibility = 4.5e-5 4.5e-5
<br>ref_p = 1.0 1.0
<br><br>gen_vel = yes
<br>gen_temp = 303.0
<br>gen_seed = 478905<br><br>Your help is highly appreciated.<br><br>Thanks<br><br>Pramod