> > Message: 6 > Date: Tue, 01 Dec 2009 07:38:29 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] amber force field in Gromacs > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4b142d45.5050...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > servaas wrote: > > Hello, > > > > I tried using the amber force field in GROMACS. I proceeded as follows: > > Determined my parameters with RED/ANTECHAMBER/tleap converted them with > > amb2gmx.pl > > (or with acpypi, problem is the same) to gromacs coordinate and topology > > files. It concerns a modified nucleotide. I minimized with steepest > > descent, everything was fine. > > When I tried running a simulation in single precision with this .mdp file > > (only nucleotide without solvent): > > > > integrator = md > > > > dt = 0.002 > > nsteps = 250000 > > nstcomm = 1 > > > > ;output > > nstxout = 1 > > nstvout = 1 > > nstfout = 0 > > nstlog = 500 > > nstenergy = 1 > > > > nstlist = 10 > > ns_type = grid > > rlist = 1.2 > > coulombtype = PME > > rcoulomb = 1.2 > > vdwtype = cut-off > > rvdw = 1.2 > > > > fourierspacing = 0.12 > > pme_order = 4 > > ewald_rtol = 1e-5 > > > > ;constraints > > constraints = all-bonds > > > > > > ; temperature coupling is on > > Tcoupl = v-rescale > > tau_t = 0.1 > > tc-grps = system > > ref_t = 300 > > > > pcoupl = no > > > > I get LINCS errors and eventually a crash. Now I tried running the same > > simulation with the same force field parameters in amber and everything was > > fine. > > I also ran the calculation in GROMACS with double precision here again > > everything was fine... I also tried running a small nucleic acid fragment > > (so no modified parameters here) > > that I created in tleap and converted to GROMACS again this crashes with > > lincs errors in GROMACS. When I look at the trajectories it is the O4' of > > the ribose who clashes with the O3'. > > > > The fact that I still get this problem with non modified amber parameters > > makes me thing there is something wrong with my .mdp file to run with amber > > FF, any suggestions? > > Strange also that double precision seems to work just fine.... > > When switching precision, are the starting configurations different? > What are the actual command lines in your procedures? It is the exact same structure, when I look at the trajectory I see the O3'-H rotate towards the O4' in the single precision trajectory they come too close and clash. In the double precision trajectory the O3'-H also rotates towards O4' but they do not come so close...
I did not include the command lines for amber and RED, please let me know if they are relevant to you. So first I use RED to determine the charges of different fragments of my molecule. The result are several mol2 files, I use tleap to combine this mol2 file with parts of existing amber fragments. I save an amber top and amber crd file. I convert this with amb2gmx or with acpypi (tried both same result in the simulation). ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro or python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro Then I add a box in gromacs: editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro I run a minimization: grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr mdrun -deffnm em (Also tried putting a position restraint step in between, did not resolve the problem) grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr mdrun -deffnm md Extra remarks: Simulation in vacuum is not realistic and the FF is not made for this but I also tried running it with counter ions and water, same result. In amber I can simulate the exact same molecule in vacuum, with same parameters without any problems. The exact same problem occurs if I start with a small natural nucleic acid sequence (3*DA), so 100% amber FF parameters (but created in amber and converted with amb2gmx.pl). Kind regards, Servaas > > Mark > > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 67, Issue 152 > ****************************************** -- 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/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/mailing_lists/users.php
