Hi, Thank everyone for your suggestions.
I have tried to put less molecule in a small box and find this works! Eventually I have solve the problem by using a larger initial box size for the random generated position and orientation. It seemed that the overall interaction of OPLS-AA between ethanes is attractive rather than repulsive, which leads to atomic clashes... The original box size was calculated from experimental density but apparently this does not work for the OPLS-AA. I had used larger initial box size previously (20% larger than experimental calculated box size) but it did not work out and then I gave up on this direction. Now, I have tried to enlarge the box size by 40% and everything works! Finally I should offer my gratitude to all of you. Thank you! Best, Phil On Tue, Sep 6, 2011 at 10:59 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 7/09/2011 12:40 AM, Phil (Yang) Song wrote: > > Hi, all > > 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. > > 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. > > > That's almost certainly inappropriate. Atomic clashes are inevitable, and > EM will not fix severe problems. > > Get a single molecule in a small box, and use genconf to replicate it. Then > use EM and equilibrate thoroughly to remove the residual ordering. Judicious > use of NPT will fix your density to whatever you want. > > Mark > > > 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 ethane molecules laid on top of each other after > minimization and infinity forces were resulted. > > 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. > > 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. > > Eventually, I am puzzled... > > 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. > > Thank you in advance! > > Best, > Phil Song > > > ================================================================================ > MDP file > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; preprocessing options > > ; title of the simulation > title = > > ; include path > include = > > ; cpp flag > define = > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; energy minimization > integrator = steep > > ; Start time and timestep in ps > tinit = 0 > dt = 0.001 > nsteps = 500 > > ; run continuation or reperforming > init_step = 0 > > emtol = 1000.0 > emstep = 0.01 > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; periodic boundary conditions > pbc = xyz > > periodic_molecules = no > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; electrostatics and vdw options > ; electrostatics method > coulombtype = PME > rcoulomb = 1.3 > > ; fourier setup for PME > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > > ewald_geometry = 3d > > ; vdw cutoff > rvdw-switch = 0 > rvdw = 1.31 > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; neighbor list options > ; neighbor list frequency > nstlist = 10 > > ; neighbor search algorithm > ns_type = grid > > ; neighbor list cut-off > rlist = 1.30 > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; thermostat and barostat > tcoupl = v-rescale > tc_grps = System > ref_t = 50.5 > tau_t = 0.5 > > pcoupl = berendsen > pcoupltype = isotropic > nstpcouple = 10 > ref_p = 1.01325 > tau_p = 1.0 > > ; Using compressibility of ethanol at 273.1 (approximately) > ; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164 > > compressibility = 1.0e-5 > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; velocty generation > gen_vel = yes > gen_temp = 50.5 > ; gen_seed = 173529 > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; > ; output control options > ; output frequency for coords, velocities and forces > nstxout = 5000 > nstvout = 5000 > nstfout = 5000 > > ; output frequency for energy > nstenergy = 5000 > ; energygrps = > > ; output frequency for log > nstlog = 5000 > > ; output options for trajectory > nstxtcout = 5000 > xtc_precision = 100000 > ; xtc_grps = > > > > ================================================================================ > ITP file > > ; Ethane: > ; Assign of the atom index > ; > ; H2 H6 > ; | | > ; H3 - C1 - C5 - H7 > ; | | > ; H4 H8 > ; > > [ moleculetype ] > ; name nrexcl > Ethane 3 > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 opls_135 1 ETH CE1 1 -0.18 > 2 opls_140 1 ETH HE2 1 0.06 > 3 opls_140 1 ETH HE3 1 0.06 > 4 opls_140 1 ETH HE4 1 0.06 > 5 opls_135 1 ETH CE5 2 -0.18 > 6 opls_140 1 ETH HE6 2 0.06 > 7 opls_140 1 ETH HE7 2 0.06 > 8 opls_140 1 ETH HE8 2 0.06 > > [ bonds ] > ; ai aj funct c0 c1 > 1 5 1 > 2 1 1 > 3 1 1 > 4 1 1 > 6 5 1 > 7 5 1 > 8 5 1 > > [ pairs ] > ; ai aj funct > 2 6 > 2 7 > 2 8 > 3 6 > 3 7 > 3 8 > 4 6 > 4 7 > 4 8 > > [ angles ] > ; ai aj ak funct c0 c1 > ; H3-C-C > 2 1 5 1 > 3 1 5 1 > 4 1 5 1 > ; H-C-H > 2 1 3 1 > 2 1 4 1 > 3 1 4 1 > ; C-C-H3 > 6 5 1 1 > 7 5 1 1 > 8 5 1 1 > ; H-C-H > 6 5 7 1 > 6 5 8 1 > 7 5 8 1 > > [ dihedrals ] > ; ai aj ak al funct c0 c1 c2 > c3 c4 > 2 1 5 6 3 > 3 1 5 6 3 > 4 1 5 6 3 > 2 1 5 7 3 > 3 1 5 7 3 > 4 1 5 7 3 > 2 1 5 8 3 > 3 1 5 8 3 > 4 1 5 8 3 > > > > -- > Phil (Yang) Song > Room 509, 590 Comm. Ave. > Chem. Dept., Boston Univ. > Boston, MA, 02215, USA > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Phil (Yang) Song Room 509, 590 Comm. Ave. Chem. Dept., Boston Univ. Boston, MA, 02215, USA
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