Hi,
I'm not sure this will help, because I'm not sure what the origin of the
problem is, but you can easily hack a copy of your .top so that a fresh run
of grompp will produce a .tpr that will match the .xtc.
Mark
On Sep 28, 2014 7:47 AM, rocwhite168 rocwhite...@163.com wrote:
Dear GROMACS
Thank you very much for the suggestion!
How do you think are there any drammatic differences between different
preassure coupling (barostats) methods implemented not only in Gromacs but
in other md packages like amber and namd? What barostat will be better for
memrbane protein simulation ?
James
Dear users.
I am doing the tutorial KALP15 in DPPC.
I heve done till the command
genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10
after that I am not able to understand wat to do and how to solvate the
system.
please can anyone expalin me in easy words how to proceed.
Dear users.
I am doing the tutorial KALP15 in DPPC.
I heve done till the command
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
and then i minimised the the system by running the command
mdrun -v -deffnm em
now i am unable to understand how to produce confout.gro
Hey gromacs users
I got the confout.gro file by running the command
mdrun -v -deffnm em -o confout.gro
and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC
0 system_shrink1.gro 5 area_shrink1.dat
but now the teminal says that
Reading.
Use of uninitialized value $box_x in
Dear gromacs users,I want to calculate the flow of water through a specific
surface area inside my simulation box. Is there any process for this? I
looked at the mailing list but could not find anything.
It would be very nice if someone can help me with this. Thanks in advance.
--
Gromacs Users
On 9/28/14 7:36 AM, Anurag Dobhal wrote:
I am simulating an RNA molecule in which first residue has a 5'-PO4 cap,
which is uncommon. I am adding the atoms and bond parameters in the .rtp
files in the existing force field directories but these parameters are not
getting saved. I am using Amber
On 9/28/14 7:41 AM, James Starlight wrote:
Thank you very much for the suggestion!
How do you think are there any drammatic differences between different
preassure coupling (barostats) methods implemented not only in Gromacs but
in other md packages like amber and namd? What barostat will be
On 9/28/14 9:14 AM, Anurag Dobhal wrote:
Hey gromacs users
I got the confout.gro file by running the command
mdrun -v -deffnm em -o confout.gro
and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC
0 system_shrink1.gro 5 area_shrink1.dat
but now the teminal says that
Dear users,
I'm going to simulate a protein. On the pdb file contents, it's said that
this protein has two chains, and missing residues and atoms. when I try to
pdb2gmx, the error messages occured. It seemed due tue the missing residue
so that i got the message error.
My question is: How can I
Hi,
There are some suggestions at
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File
Mark
On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin nizar.fku...@gmail.com
wrote:
Dear users,
I'm going to simulate a protein. On the pdb file contents, it's said that
this protein has two
Sometimes the forcefield can not directly use the residue names of a pdb
file.
In Amber forcefield, a glycine at c-terminal should be 'CGLY' instead of
just GLY.
Similarly, there is 'NGLY'. And histidine of different protonation states
have different names.
Cysteine with and without disulfide bond
Thanks Mark,
I will try swiss-Pdb viewer.
On Sun, Sep 28, 2014 at 9:45 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
There are some suggestions at
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File
Mark
On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin
Hi Mark,
Thanks for your suggestion. That's actually what I've been doing. However,
it requires modifying not only .top but also conf.gro and grompp.mdp (to
remove reference to index groups of fixed atoms that no longer exist), as
well as rerunning make_ndx. I was hoping there would be a less
Dear Mikhail,
If you are interested in a GROMOS-compatible force field for glycoproteins
(and, consequently, N-linked glycans), we've just published new
parameter sets for such biomolecules:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.23721/abstract
If you, or anyone else require any
On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168 rocwhite...@163.com wrote:
Hi Mark,
Thanks for your suggestion. That's actually what I've been doing. However,
it requires modifying not only .top but also conf.gro and grompp.mdp (to
remove reference to index groups of fixed atoms that no longer
On Sun, Sep 28, 2014 at 12:24 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168 rocwhite...@163.com wrote:
Hi Mark,
Thanks for your suggestion. That's actually what I've been doing.
However,
it requires modifying not only .top but also
On Sun, Sep 28, 2014 at 8:32 PM, rocwhite168 rocwhite...@163.com wrote:
On Sun, Sep 28, 2014 at 12:24 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168 rocwhite...@163.com
wrote:
Hi Mark,
Thanks for your suggestion. That's actually what
Yes. I'm using gmx msd with and without the -mol option. Both will
crash if I attempt to supply an index file that includes more atoms
than in .xtc.
Roc
On Sun, Sep 28, 2014 at 2:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Sun, Sep 28, 2014 at 8:32 PM, rocwhite168 rocwhite...@163.com
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