[gmx-users] free energy and fatal error

[MURAT CETINKAYA]

> Message: 1
> Date: Mon, 26 Jun 2006 12:12:49 +0200
> From: Maik Goette <mgoette at mpi-bpc.mpg.de>
> Subject: Re: [gmx-users] free energy and fatal error
> To: Discussion list for GROMACS users <gmx-users at 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