<div class="gmail_quote"><div><div class="h5"><div class="gmail_quote">Hi, all<br><div class="gmail_quote"><br>I am learning GROMACS 4.5.1 recently and encountered a problem that puzzled me for weeks. I am wondering if someone can help me with this.<br>
<br>Here is the problem: I was trying to perform a MD simulation for 216 ethane molecules in a box. I have first generated a box of ethane with random position and orientation. Then, I wanted to run a minimization for the box of ethane to get rid of close contact of the randomly ethane molecules. However, I have found that some of the <span>ethane</span> molecules laid on top of each other after minimization and infinity forces were resulted. <br>
<br>Since my mdp file was successfully used to generate other type of molecules such as acetylene and ethylene and they should be correct. Also, I have tried to use conjugate gradient instead of steepest decent for the minimization, but this effort came out to be in vain. <br>
<br>Later, I thought the topology file should be the source of error. I have carefully checked the topology file for couple of times but did not find any obvious error. I have also tried to change the charges on each atom in the ethane to 0 and then run the minimization. Again, the ethane was attracted into each other. Hence, I think the vdw could be the problem. However, the parameters of the vdw interaction are all from the opls-aa files that come with gromacs and it should be fine.<br>
<br>Eventually, I am puzzled... <br><br>I am iterating the content of the content of mdp input file and itp file in the email and also attaching the input and output of my result as a tarball. Hope someone can help me to solve this problem.<br>
<br>Thank you in advance!<br><br>Best,<br>Phil Song<br><font color="#888888"><br>================================================================================<br>MDP file<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>
; preprocessing options<br><br>; title of the simulation<br>title =<br><br>; include path<br>include =<br><br>; cpp flag<br>define =<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; energy minimization<br>
integrator = steep<br><br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.001<br>nsteps = 500<br><br>; run continuation or reperforming<br>init_step = 0<br><br>emtol = 1000.0<br>
emstep = 0.01<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; periodic boundary conditions<br>pbc = xyz<br><br>periodic_molecules = no<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; electrostatics and vdw options<br>
; electrostatics method<br>coulombtype = PME<br>rcoulomb = 1.3<br><br>; fourier setup for PME<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br><br>ewald_geometry = 3d<br><br>; vdw cutoff<br>rvdw-switch = 0<br>rvdw = 1.31<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; neighbor list options<br>; neighbor list frequency<br>
nstlist = 10<br><br>; neighbor search algorithm <br>ns_type = grid<br><br>; neighbor list cut-off<br>rlist = 1.30<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; thermostat and barostat<br>tcoupl = v-rescale<br>
tc_grps = System<br>ref_t = 50.5<br>tau_t = 0.5<br><br>pcoupl = berendsen<br>pcoupltype = isotropic<br>nstpcouple = 10<br>ref_p = 1.01325<br>tau_p = 1.0<br>
<br>; Using compressibility of ethanol at 273.1 (approximately)<br>; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164<br><br>compressibility = 1.0e-5<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; velocty generation<br>
gen_vel = yes<br>gen_temp = 50.5<br>; gen_seed = 173529<br><br>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<br>; output control options<br>; output frequency for coords, velocities and forces<br>nstxout = 5000<br>
nstvout = 5000<br>nstfout = 5000<br><br>; output frequency for energy<br>nstenergy = 5000<br>; energygrps =<br><br>; output frequency for log<br>nstlog = 5000<br><br>; output options for trajectory<br>
nstxtcout = 5000<br>xtc_precision = 100000<br>; xtc_grps =<br></font><br><font color="#888888"><br>================================================================================<br>ITP file<br><br>; Ethane:<br>
; Assign of the atom index<br>;<br>; H2 H6<br>; | | <br>; H3 - C1 - C5 - H7<br>; | | <br>; H4 H8<br>;<br><br>[ moleculetype ]<br>; name nrexcl<br> Ethane 3<br><br>[ atoms ]<br>
; nr type resnr residu atom cgnr charge mass<br> 1 opls_135 1 ETH CE1 1 -0.18 <br> 2 opls_140 1 ETH HE2 1 0.06 <br> 3 opls_140 1 ETH HE3 1 0.06 <br>
4 opls_140 1 ETH HE4 1 0.06 <br> 5 opls_135 1 ETH CE5 2 -0.18<br> 6 opls_140 1 ETH HE6 2 0.06<br> 7 opls_140 1 ETH HE7 2 0.06 <br>
8 opls_140 1 ETH HE8 2 0.06<br><br>[ bonds ]<br>; ai aj funct c0 c1<br> 1 5 1<br> 2 1 1<br> 3 1 1<br> 4 1 1<br>
6 5 1<br>
7 5 1<br> 8 5 1<br><br>[ pairs ]<br>; ai aj funct<br> 2 6<br> 2 7<br> 2 8<br> 3 6<br> 3 7<br> 3 8<br> 4 6<br> 4 7<br> 4 8<br> <br>[ angles ]<br>; ai aj ak funct c0 c1<br>
; H3-C-C<br> 2 1 5 1<br> 3 1 5 1<br> 4 1 5 1<br>; H-C-H<br> 2 1 3 1<br> 2 1 4 1<br> 3 1 4 1<br>; C-C-H3<br> 6 5 1 1<br>
7 5 1 1<br> 8 5 1 1<br>; H-C-H<br> 6 5 7 1<br> 6 5 8 1<br> 7 5 8 1<br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 <br>
2 1 5 6 3<br> 3 1 5 6 3<br> 4 1 5 6 3<br> 2 1 5 7 3<br> 3 1 5 7 3<br> 4 1 5 7 3<br> 2 1 5 8 3<br>
3 1 5 8 3<br> 4 1 5 8 3<br><br><br clear="all"></font></div><font color="#888888"><br>-- <br>Phil (Yang) Song<br>Room 509, 590 Comm. Ave.<br>Chem. Dept., Boston Univ.<br>Boston, MA, 02215, USA</font><br>
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