[gmx-users] RE: Energy Minimization

Ehud Schreiber schreib at compugen.co.il
Tue Oct 19 10:55:11 CEST 2010


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 <saipooja at gmail.com>
Subject: [gmx-users] Energy Minimization
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
	<AANLkTinomj-hzW2u+g6sA=mxQLc7q6iBWwiqj+Mx6k28 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi all,

I am using CHARMM forcefield with tables for Protein SOL interactions
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

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
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
emtol           = 1.0           ; Stop minimization when the maximum
force <
1.0 kJ/mol
nsteps          = 10000         ; Maximum number of (minimization) steps
nstenergy       = 10000         ; Write energies to disk every nstenergy
energygrps      = Protein SOL
energygrp_table = Protein SOL
; Parameters describing how to find the neighbors of each atom and how
calculate the interactions
ns_type         = grid          ; Method to determine neighbor list
coulombtype     = User  ; Treatment of long range electrostatic
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?


Quaerendo Invenietis-Seek and you shall discover.
-------------- next part --------------
An HTML attachment was scrubbed...


gmx-users mailing list
gmx-users at gromacs.org
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

End of gmx-users Digest, Vol 78, Issue 132

More information about the gromacs.org_gmx-users mailing list