Indeed I have ran into problems. The molecule blows up on me whenever I try
to calculate the energy. My input em.mdp is:
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = cg
dt = 0.002
nsteps = 1;100000
nstlist = 10
ns_type = grid
rlist = 0.8
rcoulomb = 1.4
rvdw = 1.4
the output of the program after mdrun is:
Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 2 steps.
my input .gro file is fine by visual checking using vmd, but the output
blows up with a high energy.
From: Yang Ye <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] calculation without box
Date: Sat, 11 Mar 2006 01:21:44 +0800
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It can be possibly done as you said... =) You may have your difficulty in
this but not specified in the mail.
Use nstep=1 to calculate the energy.
Yang Ye
rob yang wrote:
Hi list,
is there a way to calculate the energy of a given molecule without having
to put it in a periodic box?.. thanks
Rob
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