Anna Marabotti wrote:
Dear gmx-users,
after my last message yesterday on the gmx-user list, I contacted the
administrators of the machine on which Gromacs 4.0.7 has been installed.
We performed several checks and concluded that probably the command
mdrun_d on that machine has been badly comp
= inf
Anna
Message: 2
Date: Fri, 21 May 2010 14:44:04 +0200
From: Luca Mollica
Subject: Re: [gmx-users] stepsize too small ... but potential energy
negative!
To: Discussion list for GROMACS users
Message-ID:<4bf68014.1060...@ibs.fr>
Content-Type: text/plain; charset
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
ligand after the editconf step (i.e. I created the topology with
pdb2gmx,
created a cubic box with editconf, then I used grompp+mdrun to
perform EM).
I
Anna Marabotti wrote:
Dear Luca, dear all,
thank you for your hints. I made some trials with my systems and these are
my answers to your questions:
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
liga
Moreover,
the problem is not the potential energy, but the force that must converge.
The "inf" there about force and about atom 1 tells me that the computed
force has problems, indeed.
Which is atom 1 ? Is the protein Nter neutral or charged ? Or is atom 1
an atom from the ligand ?
Cheers
L
Dear Anna,
are you talking about a system "in vacuo" or in solvent ?
If you have placed the protein in water w/o minimizing it before
solvation, probabily an "in vacuo" minimization could be useful for your
system before moving into the solvated case. Moreover, are you sure that
the protein doe
Hello!
There are many discussions on the maillist about this...
In short, if all you want to do is normal md, it should be ok to just
proceed with that. Just check that your potential energy is negative
and everything should fine.
Otherwise, recompiling Gromacs to use double precision migh
I find getting a system minimised is often quite
tricky. There's a variety of things that can be
fiddled with, using cg with various intervals between
steps of steepest descent, running a few steps of md
(say, 10 to 100) after minimisation and then
minimising again, randomly perturbing the coordin
Hi,
What is your 'emstep' value in your mdp file? Could you try to rerun your system with a low emstep; say with emstep = 0.1
or else?
pb.
On Jul 18, 2006, at 1:13 AM, Srivastava, Dhiraj (UMC-Student) wrote:
Hi all
when i am trying to minimize my structure, i am getting following error.
Srivastava, Dhiraj (UMC-Student) wrote:
Hi all
when i am trying to minimize my structure, i am getting following error.
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
This is not an error. If your Fmax is aroun
Title: RE: [gmx-users] Stepsize too small, or no change in energy
Dear Dhiraj,
You're using single precision GROMACS which means that there is a limit to how small your forces can go, if you want to minimise further you will need to use double precision GROMACS (which will decreas
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