my command was:
/share/apps/gromacs-4.5.2/bin/grompp_mpi -f md.mdp -c
../../membed_17_npt.gro.884814.gro -t ../../membed_17_npt.trr.884814.trr -e
../../membed_17_npt.edr.884814.edr -p topol_protein_dppc_sol3_22.top -n
index.ndx -o md_0_1_22.tpr
the name of the edr file (and other NPT outputs) is
I really do not know how to get those beta-sheet structures out,
or maybe by which ways?
Any clues are warmly welcomed and appreciated.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Mark Abraham [mark.abra...@anu.edu.au]
Se
Dear All,
I was just wondering if Andersen thermostat is implemented or going to be
implemented in the recent/forthcoming versions of Gromacs.
Is there anyone who has done it otherwise and would be willing to share an
outline of the subroutines that they modified?
Thanks in advance for your help
Thanks a lot for that Justin - I fully appreciate your point, thanks
again!
-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Tuesday, November 23, 2010 3:29 AM
To: Discussion list for GROMACS users
Subject: RE
On Nov 22, 2010, at 3:09 AM, mohsen ramezanpour wrote:
> I am searching for a tutorial for learning how to do protein folding with
> Gromacs.
> Do any one know such tutorials?
Not exactly a tutorial, but you can find Gromacs input files, as well as
several hundreds of microseconds worth of MD t
On Mon, Nov 22, 2010 at 2:55 PM, Sanku M wrote:
> Hi,
>
> When using gromacs 4.5.3, I experienced two problems ( neither of which
> exist in gromacs 4.0.7 or older version like 3.3.3)
> 1. when issuing grompp command to start one of my simulations, gromacs
> 4.5.3 gives me fatal error:
>
Hi,
When using gromacs 4.5.3, I experienced two problems ( neither of which exist
in
gromacs 4.0.7 or older version like 3.3.3)
1. when issuing grompp command to start one of my simulations, gromacs 4.5.3
gives me fatal error:
'can not find atom type SNa .'
However, with gromacs 4.0.
Quoting NG HUI WEN :
> Dear Mark and Justin,
>
>
>
> I have a potentially silly question here. I have been trying to work out
> the figures from the various options of g_energy. You mentioned before
> that the bonded terms are not decomposable/require some hacking with the
> .top file. I am a bit
On 2010-11-22 13.36, wrote:
Dear gmxers,
I do not know whether this question is suitable here. If not, please
just neglect it. However, this question puzzles me greatly, that is, how
to obtain the coordinates of atom 100 with number in the frame 100 using
xdrfile in C code. Here 100
On 2010-11-22 13.27, Thomas Evangelidis wrote:
With respect to protein folding, I want to fold a 42 amino acid loop
(part of a protein domain with known structure) which has no homologous
counterpart in PDB. Ab initio servers fail to assign a compact tertiary
structure to the loop, so I would lik
Dear gmxers,
I do not know whether this question is suitable here. If not, please just
neglect it. However, this question puzzles me greatly, that is, how to obtain
the coordinates of atom 100 with number in the frame 100 using xdrfile in C
code. Here 100 is only an example for some defined a
With respect to protein folding, I want to fold a 42 amino acid loop (part
of a protein domain with known structure) which has no homologous
counterpart in PDB. Ab initio servers fail to assign a compact tertiary
structure to the loop, so I would like to see how MD tools can cope with
this problem.
On 22/11/2010 7:11 PM, andrea spitaleri wrote:
Hi,
two on five have magic error at the same time. The simulation ends
fine. Just the xtc files are corrupted. The magic error is systematic,
since I repeated the simulation 4 times and I get the same behavior
(at different time) after the continu
On 22/11/2010 11:03 PM, Adva Suez wrote:
Hello,
I'm using your KALP in DPPC tutorial to figure out how to simulate a
molecule in a membrane in GROMACS. I'm using version 4.5.2 and from
some reason I got an error in grompp whe trying generate md_0_1.tpr.
the error is:
Program grompp_mpi, VERS
Hello,
I'm using your KALP in DPPC tutorial to figure out how to simulate a
molecule in a membrane in GROMACS. I'm using version 4.5.2 and from some
reason I got an error in grompp whe trying generate md_0_1.tpr.
the error is:
Program grompp_mpi, VERSION 4.5.2
Source code file: enxio.c, line: 1097
On 22/11/10 11:09, mohsen ramezanpour wrote:
Dear All
I am searching for a tutorial for learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.
I don't think so because managing to fold a protein in a MD simulation
is no easy task. In theory,
On 22/11/2010 10:09 PM, mohsen ramezanpour wrote:
Dear All
I am searching for a tutorial for learning how to do protein folding
with Gromacs.
Do any one know such tutorials?
Please let me know them.
There aren't any, because basically no proteins fold on the time scales
that are accessible
On 22/11/2010 10:16 PM, mohsen ramezanpour wrote:
Dear All
I had a pdb file who was incomplete,there were not some atom
coordinates in the file.
I used a server who repaired it for me.
The result was a .pqr file .
Do you know any simple way for transforming .pqr file to .pdb?
I want to s
Dear All
I had a pdb file who was incomplete,there were not some atom coordinates in
the file.
I used a server who repaired it for me.
The result was a .pqr file .
Do you know any simple way for transforming .pqr file to .pdb?
I want to see the structure with Pymol and it can't read pqr form
Dear All
I am searching for a tutorial for learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.
Thanks in advance
Sincerely
Mohsen
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please s
Dear Mark and Justin,
I have a potentially silly question here. I have been trying to work out
the figures from the various options of g_energy. You mentioned before
that the bonded terms are not decomposable/require some hacking with the
.top file. I am a bit confused with that.
As mention
When I went a bit further, I found it's wrong.
Sorry.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Monday, November 22, 2010 4:50 PM
To: Discussion list for GROMACS users
Subject: RE: [g
I just tried the same way as using NA+, by
genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname
CL- -np Number_of_K
It works, u may do a try.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Jignesh
Jignesh Patel skrev 2010-11-22 08.57:
Dear all,
Can anybody tell me how to incorporate potassium ion parameters in
GROMACS for GROMOS53a6 forcefield.
Thanking you in anticipation.
With regards,
Jignesh
If you have decent parameters, add them to ions.itp
--
---
Hi,
two on five have magic error at the same time. The simulation ends fine. Just the xtc files are
corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same
behavior (at different time) after the continuing run. First time, I suspected for some I/O err
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