francesca vitalini wrote:
Dear Mark,
Thank you for your answer. I'm trying now with the position restraints
and see what happens.
However, another question came up to my mind in the mean time. I'm
using GROMACS 3.3.1 (version with mapping for reverse transformation,
I have been posting on it be
Dear Mark,
Thank you for your answer. I'm trying now with the position restraints
and see what happens.
However, another question came up to my mind in the mean time. I'm
using GROMACS 3.3.1 (version with mapping for reverse transformation,
I have been posting on it before) and for the mdrun the fl
On 30/03/2012 8:39 AM, francesca vitalini wrote:
Thank you Justin for your answer. I'm trying to add the position
restraints to my protein, but I have a problem. My topology is made of
a chain repeated twice and if I want to build the position restraints
through genrestr from a gro file, the nume
t;>> ; Dispersion correction
>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes ; assign velocities from Maxwell
>>> distribution
>>> gen_temp = 300 ; tem
e, although I never exactly figured out why.
Maybe it's worth a try for you, too?
Cheers,
Felix
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von francesca vitalini
Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion
from "all-bonds" to only "h-bonds"
> did the trick for me, although I never exactly figured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun
francesca vitalini wrote:
Hallo Felix,
thank you for your answer. I tried the constraints = h-bonds but no
change in the output. If I look at the step.pdb file that is produced
after the running I have some strange outcome. For example some of my
atoms are not recognized as part of my protein a
liche Nachricht-
Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] Im Auftrag von francesca vitalini
Gesendet: Donnerstag, 29. März 2012 15:15
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Not able to continue with Equilibration
Hi!
I'm having a
gured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -Ursprüngliche Nachricht-
> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
> Auftrag von francesca vitalini
> Gesendet: Donnerstag, 29. März 2012 15:15
> A
reff: Re: [gmx-users] Not able to continue with Equilibration
Hi!
I'm having a similar problem. I have a dimer solvated in a big box of water
plus ions that I have managed to minimize correctly (see output of minimization
at the end) but when I try to run NVT equilibration (see later) I
Hi!
I'm having a similar problem. I have a dimer solvated in a big box of
water plus ions that I have managed to minimize correctly (see output
of minimization at the end) but when I try to run NVT equilibration
(see later) I get LINCS warnings(see below) refearred to atoms which
are not in a clust
On 29/03/2012 8:22 PM, Hendry wrote:
Hi,
I am using Gromacs 4.5.4. After successful minimization by SD, I
continued with equilibration step but I got the below errors. I tried
many times with different parameters but the problem still persists. I
have given errors and md parameters of equili
>
> Good luck.
>
> ** **
>
> *Von:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> *Im Auftrag von *Hendry
> *Gesendet:* Donnerstag, 29. März 2012 11:25
> *An:* Discussion list for GROMACS users
> *Betreff:* [gmx-users] Not able to continue with E
good idea (search the
mailing list for many discussions about this topic).
Good luck.
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von Hendry
Gesendet: Donnerstag, 29. März 2012 11:25
An: Discussion list for GROMACS users
Betreff: [gmx-users] Not able to con
Hi,
I am using Gromacs 4.5.4. After successful minimization by SD, I continued
with equilibration step but I got the below errors. I tried many times with
different parameters but the problem still persists. I have given errors
and md parameters of equilibration step below. I have also provided
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