Hi,
I would allow flexible water by uncommenting the line
define = -DFLEXIBLE
and trying again; reducing the time step might also be required.
------------------------------------------------------------------------
----
Message: 4
Date: Mon, 18 Oct 2010 16:26:16 -0400
From: Sai Pooja <saipo...@gmail.com>
Subject: [gmx-users] Energy Minimization
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<aanlktinomj-hzw2u+g6sa=mxqlc7q6ibwwiqj+mx6...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I am using CHARMM forcefield with tables for Protein SOL interactions
for
alanine dipeptide.
Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard
tables for 6-12 interactions used)
Combination rule changed from '2' to '1' in forcefield.itp file.
In the energy minimization step, using mdrun the following problem is
encountered:
Polak-Ribiere Conjugate Gradients:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 10000
F-max = 2.98523e+10 on atom 4
F-Norm = 1.32072e+09
step -1: Water molecule starting at atom 1149 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to
find
certain files
cpp = /lib/cpp ; Preprocessor
; Define can be used to control processes
;define = -DFLEXIBLE
define = -DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator = cg ; Algorithm (steep = steepest descent
minimization)
emtol = 1.0 ; Stop minimization when the maximum
force <
1.0 kJ/mol
nsteps = 10000 ; Maximum number of (minimization) steps
to
perform
nstenergy = 10000 ; Write energies to disk every nstenergy
steps
energygrps = Protein SOL
energygrp_table = Protein SOL
; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
ns_type = grid ; Method to determine neighbor list
(simple,
grid)
coulombtype = User ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Any suggestions?
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20101018/355f3a
45/attachment.html
------------------------------
--
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!
End of gmx-users Digest, Vol 78, Issue 132
******************************************
--
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
