In GRO file, the atom numbers do not really matter. Just use any number you
like. It will work correctly.
mdrun will renumber atoms from 9, as it likes, automatically.
Dr. Vitaly Chaban
On Thu, May 30, 2013 at 4:57 AM, Phil wrote:
> I'm working on a .GRO file and have come across a fo
Hey,
If the gro file was built with a non-gmx program, it may be that the
numbers indeed broke the format, which then needs to be fixed. In case you
write your own program, you want to use a statement like atid = atid %1e5
to make sure it doesn't go over five digits. Correcting the format is
possi
Manual 6.7?
On Thu, May 30, 2013 at 7:05 AM, James Starlight wrote:
> Dear Gromacs users!
>
> In some discussions I've noticed that people told about usage of virtual
> sites which allow to increase time step of the simulation of such systems.
> >From manual and tutorial its not quite understand
No charges = no problem. You can trivially test this yourself with mdrun
-rerun ;-) Manual 4.1.4 talks about what RF is doing.
Mark
On Thu, May 30, 2013 at 6:38 AM, Dallas Warren wrote:
> In a system that has no charges, should we observe a difference between
> simulations using PME/Cut-offs o
Mark,
thanks for advise. As I understood for the usage of virtual sites in
typical protein-water system I should
(1) define all hydrogens as the virtual atoms (2) increase atom masses of
the hydrogens presented in the water, COOH NH2 OH and SH as well as polar
groups (3) make virtual sites for t
Dear all,
I posted some days ago an issue regarding overlap values. If any of you is
experienced with this I would appreciate some comments. Please find below
the mentioned post:
I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time
Also some questions about corrections in the mdp besides the time-step file
which should be included with the VS.
1) What constrains algorithm should I use ?
typically I use
; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even
Hi Miguel,
Sorry for not responding earlier, but the question isn't really simple :)
What you do is determining the covariance matrix from the start up to a
certain point and see for different end points what the overlap is with the
covariance matrix from the whole. This means that in all cases, t
Hmmm...
And what does the observed difference look like, numerically?
On Thu, May 30, 2013 at 10:14 AM, Mark Abraham wrote:
> No charges = no problem. You can trivially test this yourself with mdrun
> -rerun ;-) Manual 4.1.4 talks about what RF is doing.
>
> Mark
>
>
> On Thu, May 30, 2013
Things should be identical - any quantity computed from a zero charge has
to be zero :-).
Mark
On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban wrote:
> Hmmm...
>
> And what does the observed difference look like, numerically?
>
>
>
>
>
> On Thu, May 30, 2013 at 10:14 AM, Mark Abraham >wrote:
Hi Tsjerk,
Thanks for the reply! So, let me see if I am getting the things right. The
same fitting structure is used for the overlap calculation. Since the
averaged structure is used for the covariance matrices, this is the reason
why the relaxation is included. Am I right?
The overall behavior of
Hi Miguel,
The fitting doesn't play a role; it's the dynamics of the system in the
internal frame. Because the internal frame moves, you fit, so that any
contribution due to the rigid body motion is removed.
For the rest you have to look at it like this: You start out somewhere and
walk (relax) t
Hi all,
I recently ran 20ns simulation in linux cluster.
Used following script for MD simulation
#This is the first simulation MD.mdp file contains 20 ns setup
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr
mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_firs
Dear:
I've got 4 GPU in one GPU workstation. I've submit one of my job by
command:
mdrun -s md.tpr -gpu_id 01 -n -x md.xtc
I found that all the 24 CPU were occupied by this job. However, I would
like to submit another job with -gpu_id 23, how should I specify the CPU
for each job?
thank
Dear All,
I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.
I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some dis
Hi Guozhen,
I know it has been a while, BUT I am having same/similar problem with
CLAYFF. I start with a configuration optimised by CASTEP.
Have you found a solution? Did you continue using CLAYFF? I have a ClayFF.ff
available, if you want to compare.
Thanks,V
--
View this message in context:
Dear Justin and other gromacs users ,
Thank you
for your Previous reply
I Have AMD Block Edition FX8350 Processor Also I have Ubuntu 10.04 OS
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA o
"gcc" is probably still your old version. The new one would probably be called
"gcc-4.7" or similar.
Erik
On 30 May 2013, at 15:15, vidhya sankar wrote:
> Dear Justin and other gromacs users ,
> Thank you
> for your Previous
Hi GROMACS users,
GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
simulation performance enhancements and some documentation updates. We
encourage all users to upgrade their installations from 4.6 and 4.6.1.
You can find the code, manual, release notes, installation i
it seems that Gromacs update quite frequently these days..
On 05/30/2013 05:42 PM, Mark Abraham wrote:
Hi GROMACS users,
GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
simulation performance enhancements and some documentation updates. We
encourage all users to u
Dear Jiom,
Look at justines tutorial, there's example pull .mdp.
Stephan Watkins
Gesendet: Donnerstag, 30. Mai 2013 um 14:44 Uhr
Von: "gromacs query"
An: "Discussion list for GROMACS users"
Betreff: [gmx-users] umbrella sampling for two polymer interaction
Dear All,
I want to do Um
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggs wrote:
> Dear Jiom,
>
> Look at justines tutorial, there's example pull .mdp.
>
> Stephan Watkins
>
> *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr
> *Von:* "gromacs query"
> *An
Excellent work. Thank you all for working so hard!
On Thu, May 30, 2013 at 9:24 PM, Albert wrote:
> it seems that Gromacs update quite frequently these days..
>
>
>
>
>
> On 05/30/2013 05:42 PM, Mark Abraham wrote:
>
>> Hi GROMACS users,
>>
>>
>> GROMACS 4.6.2 is officially released. It contain
Hi all,
I'm trying to set-up a free energy calculation where a molecule has +2
charge in it's native state (state A) and no charge in the mutant (state
B). Since the molecule has net +2 charge, I have to add counter-ions to
neutralize the system in state A. But in order to transform it to state B
I've had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked,
there might be better suggestions though
Hello all,
I am using pdb2gmx (4.5.5 version) to create an AMBER99sb-ILDN topology
file for a peptide. It gives me only NH3+ as the N-terminus and COO- as the
C-terminus. But, I want to have the C-terminus as COOH. The C-terminal
residue is GLY.
Can anybody give me some idea how to get the GLY CO
On Thu, May 30, 2013 at 5:54 PM, Albert wrote:
> it seems that Gromacs update quite frequently these days..
We try, thanks! :-) The idea is to get these patch releases out
more-or-less monthly. This time, we spent several weeks noticing various
correctness problems with not-quite-mainstream use
Sorry, the link to the release notes should be
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.2
(Darn, I was hoping for a clean sheet, but at least this time we got to
four hours before someone noticed something was wrong!)
Mark
On Thu, May 30, 2013 at 5
Thanks for your reply, Stephan.
Did the molecule you worked with have any atoms that are isolated
(non-bonded) to the others?
Was the equilibration run in your 1st case just a way to recruit those
isolated atoms to the others in the same molecule? I suspect I might need
to add artificial bond to c
Yes, that is what i thought too.
I have one or two things to check, then will report my results.
I have been calculating latent heat of vaporisation for a series of alkanes,
and the answer is different. Been trying to work out why, if dime setting are
wrong etc. Will post my results early next
Hi,
I am wondering if there is a way I can use twice more number of replica than
the number of CPU is available so that each replica will run at 50 % CPU
usage..For example if I have 48 replica and have 24 CPUs, is it a possibility
to perform Replica exchange in gromacs ?
I was using gromacs4.
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