info in the log file.*
*For more information and tips for troubleshooting, please check the
GROMACS*
*website at http://www.gromacs.org/Documentation/Errors
http://www.gromacs.org/Documentation/Errors*
*---*
Best Wishes,
Ali Khan
--
Gromacs
Fair enough. Thank you.
On Thu, Jul 3, 2014 at 3:26 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Jul 3, 2014 7:07 PM, Ali Khan ak...@virginia.edu wrote:
Hi Everyone,
I have a simulation running with gromacs 4.6.5. Is it possible to stop
the
simulation and restart from a check
the official release is production quality.
Best Wishes,
Ali Khan
On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi GROMACS users,
The official release of GROMACS 5.0 is available!
What new things can you expect?
* GROMACS now uses a combination of *C++98* and C99
Hi all,
I don't know if anyone has experienced this problem before, but I figure I
ask. I have several times run a simulation on a 135A x 135A POPC membrane
acquired fro the charmm-gui website. I wanted now to simulate one that was
slightly larger (150A x 150A). I made the larger membrane on
= 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
On Thu, Jun 5, 2014 at 2:36 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/5/14, 2:11 PM, Ali Khan wrote:
Hi all,
I don't know if anyone has experienced this problem before, but I figure I
ask. I have
1000
kj/mol/nm, but I still get the error during temperature equilibration.
On Thu, Jun 5, 2014 at 2:36 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/5/14, 2:11 PM, Ali Khan wrote:
Hi all,
I don't know if anyone has experienced this problem before, but I figure I
ask. I have several
:47 PM, Ali Khan wrote:
I am using the charmm36 force field.
*My energy minimization .mdp file:*
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization
Is there a difference between Potential-switch and Potential-switch-verlet?
On Thu, Jun 5, 2014 at 5:12 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/5/14, 4:57 PM, Ali Khan wrote:
Justin,
4.6.5 does not have Potential-switch-Verlet. When I added the other
changes, I still had the same
I used to have this problem in pymol as well. When I upgraded pymol to
version 1.7, the problem was fixed and the whole protein would be
displayed.
On Wed, May 28, 2014 at 10:19 PM, bharat gupta bharat.85.m...@gmail.comwrote:
I checked the structure in VMD, it shows all the chains now but the
...@chem.ox.ac.uk
wrote:
Hi Ali,
And what would you expect in this case, based on the definition of
concentration?
Erik
On 14 May 2014, at 04:11, Ali Khan ak...@virginia.edu wrote:
Sorry Mark,
I did not mean 201, 000 atoms; I meant 201 potassium atoms vs 232
potassium
atoms. Its a small
;-) concentration =
quantity / volume. From the factor of ~1000, probably you're inputting box
sizes in A instead of nm, or vice-versa, somewhere.
Mark
On Tue, May 13, 2014 at 8:43 PM, Ali Khan ak...@virginia.edu wrote:
Hey,
I generated a membrane in charmm-gui that I will be simulating
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