> Message: 1 > Date: Mon, 26 Jun 2006 12:12:49 +0200 > From: Maik Goette <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] free energy and fatal error > To: Discussion list for GROMACS users <gmx-users@gromacs.org>
I am using GROMACS 3.2.1. > > Hi > > Are those atoms mentioned, perturbed ones? Yes, all atoms are perturbed. > I think, it has nothing to do with the error, you experience, but > delta_lambda should be 1/number of steps, if you want to do TI from 0 to 1. I follow the solvation FE tutorial by Dill group. These are the parameters that they provide > Anyway, maybe you should look at the energies on these atoms and perhaps > recheck your bonded parameters... dgdl file shows an increase like this (for init and delta lambda =0): 0 58.799 0.001 -3923.71 0.002 -5081.52 0.003 -4004.63 0.004 -4382.1 0.005 -6933.78 0.006 -7533.55 0.007 -158.663 0.008 -7881.4 0.009 -776183 0.01 nan 0.011 nan 0.012 nan 0.013 nan 0.014 nan 0.015 nan 0.016 nan 0.017 nan 0.018 nan 0.019 nan > More details, like your mdp-file, would be helpful. Here is the full input file: title = NVT_EQ in vacuo cpp = /lib/cpp include = -I/../EM/ integrator = sd tinit = 0 dt = 0.001 nsteps = 10000 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 100 nstxtcout = 1000 xtc_precision = 1000 xtc_grps = Protein energygrps = Protein nstlist = 10 ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t = 10 ;0.1 in tutorial, but this may be better ref_t = 300 ;pbc = xyz rlist = 1.4 coulombtype = Shift rcoulomb = 1.2 rcoulomb_switch = 1.0 epsilon_r = 1.0 vdwtype = Shift rvdw = 1.2 rvdw_switch = 1.0 constraints = none ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 > > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > MURAT CETINKAYA wrote: > > Hi, > > > > I am trying to calculate solvation free energy of a non-standard residue and I > > have problems in vacuum runs. > > > > I defined a dummy atom for every single atom in the molecule (0 charge and > > non-bonded parameters) and I input every single bonded interaction values > > manually (in order to prevent any errors resulting from that). > > > > I minimized my molecule with l-bfgs and steep. If do free energy = no, I can do > > my NVT run in vacuo without any problems. However, when I set: > > > > free_energy = yes > > init_lambda = 0.0 > > delta_lambda = 0 > > sc_alpha = 0.5 > > sc-power = 1.0 > > sc-sigma = 0.3 > > > > I get the following error: > > step 0Warning: 1-4 interaction between 21 and 23 at distance larger than 2.4 nm > > These are ignored for the rest of the simulation > > turn on -debug for more information > > Fatal error: ci = -2147483648 should be in 0 .. 63 [FILE nsgrid.c, LINE 218] > > > > As I said, every bonded interaction value is entered manually (A = B values) and > > structure seems minimized. > > > > Any ideas appreciated > > thanks > > Murat CETINKAYA, M.Sc. > > BioNanoMaterials Group, > > Dept. of Engr. Science and Mechanics, > > The Pennsylvania State University, > > University Park, PA 16802 > > office: (814) 863 9967 > > web: www.personal.psu.edu/muc176 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
