Hi,
I try to add a dummy atom in my small molecular pdb and topology file.
(attached files)
But the MDS process still shut down.
The msg. is
[1]+ Exit 255nohup mdrun -v -deffnm npt_cmplx
Could you give me some suggestions for dealing with the problem.
Thaks a lot.
Best,
hi
I installed gromacs through the synaptics package manager in ubuntu 10.10
Since I am new to linux. So after installation when I tried to run the
example tutorials available in tutor folder, its not running. When I tried
to run the program water the .tdr file is not created while executing the
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing your message to the list and would ask that all
further discussion be sent there. See comments below.
Yanping Fan, Liza (Dr) wrote:
Dear Justin:
Good day.
I found your comm
On 2011-02-27 21.49, aldi asmadi wrote:
Many thanks David.
Just want to confirm that I understand how to calculate the monomer
correctly. So I put the single molecule inside a large cubic box, say
with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the
same cut-off parameters as
Many thanks David.
Just want to confirm that I understand how to calculate the monomer
correctly. So I put the single molecule inside a large cubic box, say
with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the
same cut-off parameters as the ones that I apply during my bulk
simul
On 2011-02-27 21.20, aldi asmadi wrote:
Dear all,
This may sound obvious and normally I would know how to address the
following question. However, I would like to ask for your opinion.
If we are simulating bulk liquid of hydrocarbon using the shell
polarizable model, is it possible to have a po
Dear all,
This may sound obvious and normally I would know how to address the
following question. However, I would like to ask for your opinion.
If we are simulating bulk liquid of hydrocarbon using the shell
polarizable model, is it possible to have a positive value for the
potential energy? In
Please note submission deadline extended to March 18, 2011
(apologies if you receive multiple copies of this call for papers)
#
IEEE WETICE 2011
2nd International Track on
Collaborative Modelin
Hello,
I want to calculate the excess chemical potential of one dissolved molecule
within an liquid system. The excess chemical potential should be delta G. The
equation for delta G is given in manual:
With -fee an estimate is calculated for the free-energy difference with an
ideal gas state:
najwa drici wrote:
hi all
Anybody guide me in installig the PROCHECK software and how to run it ??
This list is for Gromacs-related questions. Consult whatever documentation
Procheck provides and make use of whatever support resources they offer.
-Justin
best regards
--
==
hi all
Anybody guide me in installig the PROCHECK software and how to run it
??
best regards
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leila separdar wrote:
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for
generating .top and .gro files for 1000 argon atoms, in topology file I
have seen another atom O with mass 1.48594e-41 as below I do not know
what to do.I do not confront with such problems when I had
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for
generating .top and .gro files for 1000 argon atoms, in topology file I have
seen another atom O with mass 1.48594e-41 as below I do not know what to
do.I do not confront with such problems when I had 4.0.7 version of gromacs.
p
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