Justin,
Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.
Nothing changed. I suggest you to try it by yourself.
Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.
mustafa
This topology defines the [moleculetype] name as "Methanol," which is the
name
that needs to
n list for GROMACS users
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mustafa bilsel wrote:
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
>
0
Message: 7
Date: Fri, 07 Jan 2011 12:41:27 +1100
From: Mark Abraham
Subject: Re: [gmx-users] methanol simulation error
To: Discussion list for GROMACS users
Message-ID: <4d266f47.5000...@anu.edu.au>
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On 7/01/2011 12:31 PM, mus
Hi all,
I try to make a simulation in methanol. I use gromos43a1 forcefield.
My command follow,
pdb2gmx -f xxx.pdb
editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro
genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro
When grompp for minimization it gives an error:
Atomtype CM
Dear Mark,
so, what should I do?
mustafa
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Hi all,
I have the following error in grompp before energy minimization:
No such moleculetype SOL
I have used grep to count the methanol molecules and added SOL 291 comment
in .top file to tell the number of methanols.
What is missing there?
Note: I have used pdb2gmx -f xxx.pdb , that is, I haven
Hi all,
Could you tell me a program to obtain topol.top for a CNT?
In CNT.pdb residues are efined as UNK.
best wishes
mustafa
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Hi all,
At the end of the minimisation I obtained potential energy value
approximately -40,000 and I see the following warning
Stepsize too small, or no change in energy.Converged to machine precision,
but not to the requested precision Fmax < 10
As far as I know for succesful minimisation potenti
Hi Justin,
maybe I am making a mistake with installation. What I am doing is this:
I am creating a diretory called DSSP, then I write
rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/
on the terminal, and then file transfer starts. Then I write export
DSSP=/home/m/DSSP/dssp (pointing the ex
Hi,
What is the meaning of the below message after I completed minimization?
Does it mean minimization is successful?
In my input parameters nsteps=10,000,000 but minimization stops at about
14,000 th step. Is 10,000,000 very large? What is the typical value for it?
And also what is the meaning of
l 2> /dev/null
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-----------
mustafa bilsel wrote:
> Hi,
> I have a problem with dssp programme.
> I have the pro
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
command
Hi,
I have a problem with dssp programme.
I have the programme in /home/m/DSSP. When I write
export DSSP=/usr/local/bin
and then I check /usr/local/bin I couldn't see dssp.
How can I handle this problem. I have caheceked gromacs website
export DSSP=/path/to/dssp
setenv DSSP /path/to/dssp
command
Hi,
1. How can I learn the box shape and size of a completed simulation?
2. I want to keep going the previous completed energy minimization by
increasing nsteps. How can I do this?
Best wishes
Mustafa
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Hi,
I want to write the means of every 100 potential energies into an output
file.
Is there an option in Gromacs to do this?
Best wishes
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Mustafa Bilsel
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Hi,
when I tried to make energy minimisation, I see following error. My
parameters are at the end of the email. What should I do?
Fatal error:
Atomtype HW not found
Best wishes
Mustafa
MY EM.MDP
integrator= steep
nsteps=200
nstlist=10
rlist=1.0
coulombtype=pme
rcoulomb=1.0
vdw_type=cut-off
rvd
Hi all,
I would like to simulate (VPGVG)18, but it is pdb isn't in protein data
bank. Where can I find it? OR How can I simulate it under this condition?
Best wishes
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Dear Lina,
could you express these commands clearly? I am a new user!
editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_
box.gro -center x/2 y/2 z/2 -box x y z
genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o
they_are_in_the_same_box_now.gro -p topol.top
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gmx-users
Hi,
when I choose different box types and draw them by Pymol, I see no visual
difference between them. At least cubic must be different from the others.
What is the reason for this?
best wishes
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