lina wrote:
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar <[email protected]> wrote:
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-
pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr
The minim.mdp file =
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
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
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1.0
emtol = 1.0
If mdrun could not converge to 1000, setting a target of 1 will not solve
anything. The OP should refer to:
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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