On 1/18/14, 7:56 PM, rankinb wrote:
What are the formatting requirements for tables to be used as user-defined
potentials? I found the example tables, but cannot find the details in the
manual. It would be useful to have the requirements so I can save the
tables in the correct format when gen
Dear experts,
I converted a trajectory (.trr) containing a simulation of tip4ew water to
.gro format. In the resulting .gro file, there are velocities also for the tip4
virtual sites MW. This confuses me, since these sites have no mass. How is this
velocity calculated? I have been under the im
What are the formatting requirements for tables to be used as user-defined
potentials? I found the example tables, but cannot find the details in the
manual. It would be useful to have the requirements so I can save the
tables in the correct format when generated. Otherwise, does anyone have
any
Justin's suggestion sounds reasonable. Your approach would have to have
enough water that there is no perturbation upon the water interacting with
the bilayer from the water-vacuum interface. That seems prohibitive to
compute and/or demonstrate...
Mark
On Sat, Jan 18, 2014 at 9:05 PM, Guangwei J
On 1/18/14, 3:05 PM, Guangwei Jiang wrote:
Hi, Mark,
I hope to introduce the ions into two water compartments above and below the
lipid bilayers. But with the vacuum, I can block the ions flowing into the
other side. This may overcome the case from periodic boundary condition.
But I need to
On 1/18/14, 2:20 PM, rankinb wrote:
When running grompp, I am receiving the error "No molecules were defined in
the system." I have a relatively simple topology and .gro file. I cannot
locate the source of the error. Does anyone have any suggestions? Here is
an example of the .gro and .top
On 1/18/14, 3:14 AM, Mahboobeh Eslami wrote:
dear justin
I thank you for your friendly guide
Can I assume some of torsion steady and don't change them for getting results
better of docking ? can i reduce rotatable bonds for my ligand in docking
process then do MD simulation?
if i reduce rotata
On 1/17/14, 8:06 PM, Rini Gupta wrote:
Dear gmx-users,
Thanks for the reply.
That means if I will use the frames generated by script (setup-umbrella.py)
it will not generate a sufficient overlap between adjacent
windows for this system?
What I'm saying is that I know the scripts, input fil
Hi, Mark,
I hope to introduce the ions into two water compartments above and below the
lipid bilayers. But with the vacuum, I can block the ions flowing into the
other side. This may overcome the case from periodic boundary condition.
But I need to have such a stable structure with vacuum. Do y
Hello to everybody,
I am performing a simulation of a lipid membrane made of DPPC molecules in a
water solvent and I am fixing certain surface tension.
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = surface-tension
; Time constant (ps), compressibility
Hi Mark,
the reason why I am confused is, that I thought cmake checks if
everything is fine or not. So at the point I tried "cmake .." for the
first time, cmake started all these tests and finally I got the answer I
should install FFTW3 and so I did. I did this with typing "make".
Because "ma
When running grompp, I am receiving the error "No molecules were defined in
the system." I have a relatively simple topology and .gro file. I cannot
locate the source of the error. Does anyone have any suggestions? Here is
an example of the .gro and .top file that I am using. Thanks.
HSb
Hi,
I am trying to install Gromacs 4.6.5 on Kubuntu. My Kubuntu skills are not
> that good, so I kept close to the Install Instructions. I skipted the
> "Quick
> and Dirty Instrucitons" and now I should be at the point "4.1 Configuring
> with CMake". When I insert "cmake ..", I recieve:
>
>
> Can
Hi,
See g_rms -h first ;-)
Mark
On Sat, Jan 18, 2014 at 3:17 PM, Ahmet yıldırım wrote:
> Dear users,
>
> How do Gromacs choose the reference structure for the fit the trajectory?
> For example:
> g_rms -f traj.xtc -s topol.tpr
>
> The reference structure is first frame (-dump 0:closest to the
Hi,
Why are you trying to maintain a region of vacuum while changing the
density of the rest?
Mark
On Sat, Jan 18, 2014 at 3:02 PM, Guangwei Jiang
wrote:
> Thanks, Justin!
>
> But I am still puzzled about the way to do equilibration without NPT.
>
> How can we realize the equilibration for a r
Hi,
No, those are long out of date. That page has been removed for the upcoming
5.0 release of GROMACS.
Please check out http://www.gromacs.org/Documentation/Tutorials or on
Google for more up-to-date material.
Mark
On Sat, Jan 18, 2014 at 5:06 AM, John Doe wrote:
> Hi All,
>
> Are the tutor
Thanks Justin I appreciate you help...Your comments made it clear...
Steve
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Hi guys,
I am trying to install Gromacs 4.6.5 on Kubuntu. My Kubuntu skills are not
that good, so I kept close to the Install Instructions. I skipted the "Quick
and Dirty Instrucitons" and now I should be at the point "4.1 Configuring
with CMake". When I insert "cmake ..", I recieve:
Can anyone
Dear users,
How do Gromacs choose the reference structure for the fit the trajectory?
For example:
g_rms -f traj.xtc -s topol.tpr
The reference structure is first frame (-dump 0:closest to the first frame)
of the trajectory for above command?
--
Ahmet Yıldırım
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Gromacs Users mailing list
*
Thanks, Justin!
But I am still puzzled about the way to do equilibration without NPT.
How can we realize the equilibration for a reasonable density in such vacuum
scheme?
Forgive me the stupid question. Thanks very much!
Regards,
Guangwei
From: gromac
dear justin
I thank you for your friendly guide
Can I assume some of torsion steady and don't change them for getting results
better of docking ? can i reduce rotatable bonds for my ligand in docking
process then do MD simulation?
if i reduce rotatable bonds, i will get much better results of d
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