If you've done PCA, you should get an output vector anaylsis as .xvg. Aside this also breaks things into the x,y,z components for the first 8 or so vectors (so 4 line graphs of energy versus time including the total energy), along with 2D plots you can generate. You would then already have what
Thank you, David and Erik. The problem has been solved.
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Hi,
to follow up on this, the simulation with "Reaction-Field-nec" under
4.5.3 has completed. The final area is 0.60 nm^2 (see
http://redmine.gromacs.org/issues/1400 for the plot). Lutz, you
mentionned you tried a simulation with nstlist=1, could you give
feedback on redmine?
Best,
Patrick
On 12/20/13 4:14 PM, unitALX wrote:
Its true, so I did it! and looked at the resulting .gro files in VMD.
I saw that
*-vsite hydrogen *virtualizes only the non-aromatic hydrogens
*-vsite aromatics *virtualizes all hydrogens, aromatic and otherwise.
I guess therefore that one can
Hello,
I'm having trouble with the GROMACS regression test hanging with a GROMACS
built with a GCC/OpenMPI/OpenBLAS/FFTW toolchain, when MPI support is enabled
(both with and without OpenMP support).
The tests work fine when I'm using the exact same build procedure, except for
enabling MPI supp
Its true, so I did it! and looked at the resulting .gro files in VMD.
I saw that
*-vsite hydrogen *virtualizes only the non-aromatic hydrogens
*-vsite aromatics *virtualizes all hydrogens, aromatic and otherwise.
I guess therefore that one cannot, for example, virtualize *only* the
ar
yes that was the .top file i have used. ok..
Thank you!
On Fri, Dec 20, 2013 at 2:23 PM, Justin Lemkul wrote:
>
>
> On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
>
>> Justin,
>>
>> i went for the option 4 that u pointed out. let me explain what i did,
>>
>> i converted the .pdb file in to .gro
Dear all,
I have found that the GAFF force field is used in concert with the AMBER
fore fields. Since both force fields use the same [ defaults ] section
in the forcefield.itp files, I think GROMACS can come up with nonbonded
parameters between these force field.
But since both force fields us
On 12/20/13 12:24 PM, unitALX wrote:
Hello again!
Another question about -vsite:
does *-vsite aromatics * also include the hydrogens that could be
virtualized by *-vsite hydrogens*? Or should I say *-vsite hydrogens
aromatics* to virtualize both?
-vsite hydrogens should also encompass arom
On 12/20/13 2:20 PM, Sidath Wijesinghe wrote:
Justin,
i went for the option 4 that u pointed out. let me explain what i did,
i converted the .pdb file in to .gro by using.
editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90
then i use the text editor as follows.
Include forcef
Justin,
i went for the option 4 that u pointed out. let me explain what i did,
i converted the .pdb file in to .gro by using.
editconf -f test.pdb -o test.gro -box 18 18 18 -angles 90 90 90
then i use the text editor as follows.
Include forcefield parameters
#include "oplsaa.ff/forcefield.itp
Hi Justin,
Something along these lines would have been useful to me:
Addition to a sentence from Section 6.9.2 User-specified potential functions:
"...The x should run from 0 to rc + 1 (the value of table-extension can be
changed in the .mdp file),
but the value of table-extension and the lengt
On 12/20/13 8:14 AM, Alec Zander wrote:
Hello!
I'm pretty new to Gromacs. I'm running Gromacs 4.6.5 and I've been trying
out the -vsite aromatics on my protein to achieve a 4fs timestep, and I am
happy with the results. Can -vsite also be used for ligands in a ligand +
protein simulation? Woul
Hello again!
Another question about -vsite:
does *-vsite aromatics * also include the hydrogens that could be
virtualized by *-vsite hydrogens*? Or should I say *-vsite hydrogens
aromatics* to virtualize both?
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View this message in context:
http://gromacs.5086.x6.nabble.com/vsite-and-protein-
On 12/20/13 11:10 AM, vidhya sankar wrote:
Dear Justin ,
Thank you for your Previous reply.
I am Doing Simulation of assembly of Cyclic Petide in POPC membrane
For that I need to calculate Free energy for Stability of Assembly.
You suggested the Umbrella sampling
But Ap
On 12/20/13 12:09 PM, ploetz wrote:
Hi Justin,
Thanks for your reply. I agree with you that the .mdp file rlist=rcoul=rvdw
cutoff is really being applied,
but the documentation in the manual about tabulated interaction functions does
not
give me the impression that that is the intent. It rea
Hi Justin,
Thanks for your reply. I agree with you that the .mdp file rlist=rcoul=rvdw
cutoff is really being applied,
but the documentation in the manual about tabulated interaction functions does
not
give me the impression that that is the intent. It reads like the user can have
different cut
Dear Justin ,
Thank you for your Previous reply.
I am Doing Simulation of assembly of Cyclic Petide in POPC membrane
For that I need to calculate Free energy for Stability of Assembly.
You suggested the Umbrella sampling
But Aprt from that i wish to do
Free energy perturbat
On 12/19/13 7:33 PM, Robert Darkins wrote:
On 19/12/13 23:31, Justin Lemkul wrote:
On 12/19/13 6:14 PM, rdwducl wrote:
Thanks for the reply Justin but I'm confused. Why must the atoms be bonded?
Ultimately I plan to model micellisation whereby surfactants, which only
interact with each ot
Hello!
I'm pretty new to Gromacs. I'm running Gromacs 4.6.5 and I've been trying
out the -vsite aromatics on my protein to achieve a 4fs timestep, and I am
happy with the results. Can -vsite also be used for ligands in a ligand +
protein simulation? Would this introduce any problems with ligand be
Have you tried the first suggestion too ??
If even that does not worked then something wrong with your system.
On Fri, Dec 20, 2013 at 5:06 PM, Nidhi Jatana wrote:
> I tried increasing the grid spacing by setting -bin from default of 0.02 to
> 0.04 and decreased it as well to 0.01. Butives the
Hi Gromacians
Sorry for my previous post. I found the updated version by Justin. Thank you
On Fri, Dec 20, 2013 at 12:58 PM, Vinothkumar Mohanakrishnan <
kmvin...@gmail.com> wrote:
> Hi Gromacians
>
> I want to perform the tutorial Insertion of methane in water by David
> Mobely. But, unfortuna
Hi Gromacians
I want to perform the tutorial Insertion of methane in water by David
Mobely. But, unfortunately the link (
http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial)
is broken. Where can i find the tutorial? I would like to know if there is
any update on this? (
I tried increasing the grid spacing by setting -bin from default of 0.02 to
0.04 and decreased it as well to 0.01. Butives the same of no help. It
still gives the same error.
On Fri, Dec 20, 2013 at 4:19 PM, bipin singh wrote:
> You may try to produce the xpm matrix for small portion of your tr
You may try to produce the xpm matrix for small portion of your trajectory
(using -b and -e option) and then try xpm2ps on it to check whether it
works for small size xpm matrix or not.
OR you can increase the grid spacing with -bin option of g_densmap while
generating the xpm matrix for the whol
How do you fix the matrix size? Should I do it while generation of .xpm
file or while converting it to .eps and using which option?
Regards
Nidhi
On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner wrote:
> On 12/20/2013 10:09 AM, bipin singh wrote:
>
>> Not sure, might be something going wrong d
On 12/20/2013 10:09 AM, bipin singh wrote:
Not sure, might be something going wrong due to large dimension of your
matrix. Which Gromacs version you are using. Others may provide some clues.
I just tried with a 483 x 486 matrix which went smoothly.
You could try to narrow down the problem.
See w
I am using gromacs version 4.6.
On Fri, Dec 20, 2013 at 2:39 PM, bipin singh wrote:
> Not sure, might be something going wrong due to large dimension of your
> matrix. Which Gromacs version you are using. Others may provide some clues.
>
>
> On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana >wr
pdb2gmx adds hydrogens if they are not present, which will be done in the
L-form. If you already have hydrogens you should be able to maintain the
residues in D-form.
Cheers,
Erik
On 20 Dec 2013, at 09:56, David van der Spoel wrote:
> On 2013-12-20 07:23, hummingbird wrote:
>> I am doing a
Not sure, might be something going wrong due to large dimension of your
matrix. Which Gromacs version you are using. Others may provide some clues.
On Fri, Dec 20, 2013 at 10:04 AM, Nidhi Jatana wrote:
> Dear Sir/Madam
> Please find attached the file containing the error.
>
> Thanking you
>
> Re
Dear Hector,
your contribution is unrelated to this thread of conversation.
Please choose an appropriate subject line (e.g. "installation problems
with CUDA") and repost your question to the list.
Thanks,
Carsten
On 12/20/2013 07:55 AM, Hector Manuel Manzanilla Granados wrote:
Hi, I need s
On 2013-12-20 07:23, hummingbird wrote:
I am doing a simulation of a system including a peptide made up of 36 D-amino
acid residues. I am a new user and have no idea how to process D-amino acid.
When I try pdb2gmx, all residues are changed to L-type in the output GRO
file.
Could anybody help?
Tha
Hi, I need some help.
In these days, I install one NVIDIA target (GTX 760 on UBUNTU 12.04),
together with
toolkit 5.5 of CUDA. Apparently CUDA runs fine, the problem is that
I can't to compile GROMACS in CUDA, I think that have some mistake in
the
installation of cuda, may I somebody help me
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