Hi all, I know there has been a *lot* of discussion on the mailing list on using freezegrps and potential pitfalls, but after having read much of this discussion the past couple of days and the manual I still find myself with questions and problems I'm hoping someone can help with.
What I want to do, specifically, is have my protein frozen (*not* just constrained with some large force, I need actual freezing of every protein atom) but have the solvent still react to the frozen protein. The purpose behind this is to compare the water behavior near a particular part of a protein when it is dynamic and when it is not and thereby learn something about the "communication" between protein and solvent in this case. However, it seems that I'm not finding a rational set of mdp options to allow this, at least not a set for which dynamics will run with any speed. I have tried many of the things people have discussed on the mailing list, including turning off constraints, turning off pressure coupling, reducing the Protein heat bath temperature to 0 K, and using energygrp_excl. Here are the parameters I just tried: ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; integrator = md nsteps = 1000000 dt = 0.001 nstxout = 1 nstvout = 1 nstxtcout = 1 nstenergy = 1 nstlog = 1 continuation = yes constraints = none ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 0 300 pcoupl = no pbc = xyz DispCorr = EnerPres gen_vel = no freezegrps = Protein freezedim = Y Y Y ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; This ran, but *incredibly* slowly (I'm using a single 32 processor node, and only got 255 steps in 10 wallclock minutes). From the discussions I've read on the mailing list it seems that PME is somewhat less than ideal for simulations involving frozen atoms, but I used PME for electrostatics in my non-frozen simulations and would like to keep that consistent if possible (I do get a grompp warning of course). I am also getting warnings in the log file like: "DD step 254 vol min/aver 0.183! load imb.: force 2395.3% pme mesh/force 1.243" which I believe must be due to the frozen protein causing difficulties with domain decomposition. Can anyone offer any advice regarding these issues? I know this has been discussed often, but nothing I'm finding in the archives is particularly relevant. -- ---------- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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