Roland Schulz wrote:
Please make sure that the error exists in the latest version. Either
4.5.1 or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.
Please make sure that the error exists in the latest version. Either 4.5.1
or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.
On Tue, Sep 28, 2010 at 9:01
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Hello,
I am really curious that amber has support for Room Temperature Ionic
liquids ? Can you please provide me a reference how this force field
works for this kind of liquids.
/Flo
On 09/28/2010 03:01 PM, Alep Latep wrote:
> Dear Gromacs Users
Dear Gromacs Users and Developers,
I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the an
Arik Cohen wrote:
In continuation with my previous e-mail, I'm sorry to continue bothering
you with this but after reevaluating, it seems that problem might just
be with the amber forcefield after all as I manged to run grompp just
fine and to start the minimization by applying the OPLS forc
In continuation with my previous e-mail, I'm sorry to continue bothering
you with this but after reevaluating, it seems that problem might just
be with the amber forcefield after all as I manged to run grompp just
fine and to start the minimization by applying the OPLS forcefield(with
another
Thanks again for the ultrafast response.
1. The extra '.' is a typo. (I apologize for that). In the command the
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 wit
On 25/04/2010 6:28 AM, Arik Cohen wrote:
Thank a lot for your very fast response !. Here are the requested details:
1. Version 4.07 is being used.
2. Upgrading from version 4.04 to 4.07 doesn't help.
3. The grompp command given is:
grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Comple
I suppose the next set of questions to ask would be:
1. How was Gromacs compiled? What options were specified?
2. Does every instance of grompp fail? Do other inputs work? What does "grompp
-h" do?
3. Does grompp seg fault with totally different systems (different force
fields)?
-Justin
Thank a lot for your very fast response !. Here are the requested details:
1. Version 4.07 is being used.
2. Upgrading from version 4.04 to 4.07 doesn't help.
3. The grompp command given is:
grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top
-o 1bgq_Complex_b4ion..tpr
4.
On 24/04/2010 7:28 AM, Arik Cohen wrote:
I'll be most thankful if any one would be able to help me with the
following problem.
Giving more complete information will give you a much better chance.
It's not our job to be the family doctor and ask questions :-)
What GROMACS version is it? Does
I'll be most thankful if any one would be able to help me with the
following problem.
While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error. The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was runn
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