On 12/06/10, "Shi Wenxiong (Dr)" wrote:
>
>
>
>
>
>
>
>
>
>
>
>
> I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you
> will get one xtc data.
>
>
>
>
Indeed, or circumvent the problem with appropriate use of mdrun -append
Mark
>
>
>
>
>
>
>
>
Please check if your stand-alone mopac binary works properly. Also
check if the mdrun binary is linked against the libmopac.a
Gerrit
Message: 2
Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST)
From: vidhya sankar
Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
To: gmx-users@gromacs
I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you will
get one xtc data.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of shiva birgani [sh.birg...@gmail.com]
Sent: Monday, December 06, 2010 3:16 PM
To: gmx-
Dear Justin
I had a crashed run and continued it by tpbconv and mdrun. After that in
order to analysis the results of new MD run I used of this command
trjcat -s md2.tpr -settime
But when I want to compute RMSD, DSSP, ... I do not know how I can put
together the results of MD1 (crashed run) and MD2
Dear Gerrit sir,
Thank you for your previous reply i tried as u said with -nt 1
option in mdrun but still i have got hte following error when i run mdrun_d
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 2
QMlevel: PM3/STO-3G
Program mdrun_d, VERSION 4.5.3
Source
Thank you all. At least now I have an idea of the starting point.
On Sun, Dec 5, 2010 at 12:31 PM, Thomas Piggot wrote:
> I would tend to agree with Justin rather than Itamar. The GROMOS DNA
> parameters are not especially good (see
> http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends
Hi,
No. But I hope to get it done this week. Thanks for the reminder.
Erik
Robin C. Underwood skrev 2010-12-05 19.19:
Hi All:
Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506 wate
I would tend to agree with Justin rather than Itamar. The GROMOS DNA
parameters are not especially good (see
http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you
are wanting to look at. Another option (rather than CHARMM, which for
what it is worth is the force field I would
On 05/12/10 19:41, Justin A. Lemkul wrote:
Please keep all Gromacs-related correspondence on the gmx-users list. I
am not a private help service.
I do not do polymer simulations, nor do I have any real clue as to how
to help you, aside from suggesting the following, which may or may not
be rele
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service.
I do not do polymer simulations, nor do I have any real clue as to how to help
you, aside from suggesting the following, which may or may not be relevant:
http://www.gromacs.org/Documenta
Hi All:
Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506 waters I get the following nhbdist output, which appears to neglect pbc
since there are such a large number of unbound donor-H
Dear all,
I come back to you with my problem between -chargegrp and -nochargegrp with
new results which are contradict my previous
findings. Indeed, in my previous message i have suggested that the
discrepancies between -chargegrp and -nochargegrp in
my simulations of a 25 AA peptide in TIP3P wate
On 05/12/10 13:20, Justin A. Lemkul wrote:
ms wrote:
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the
force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO, the
Raymond.nuist wrote:
Dear users
Here is my problem:
I just changed my GMX version from 4.0 to 4.5.
But the task was in a Segmentation fault, whileI can "mdrun" it
well in 4.0 environment .
Providing an .mdp file and a description of your system would be useful.
ms wrote:
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
hom
Amit Choubey wrote:
Hi all,
This is a question unrelated to gromacs but would pose it anyway to get
some hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could someone
please refer to a relevant forcefield/tutorial for simulation of lipids
with DNA?
I wou
Hi Amit,
The GROMOS force field had both DNA and lipids parameters, hence you can use
it in your simulations. Moreover, there are new lipids parameters by David
Poger and Alan Mark which I should give better results compared to the old
set.
Good luck.
On 5 December 2010 18:09, Amit Choubey wro
I would use grep and cut to take the atom numbers of the residues I want to
restrain and direct them into an index file with [res_sol] at the top. Then
use genrestr to generate restraints for these atoms using the -n option.
Then conditionally include this restraint file (.itp file) in my topology
Dear users
Here is my problem:
I just changed my GMX version from 4.0 to 4.5.
But the task was in a Segmentation fault, whileI can "mdrun" it well in
4.0 environment .
Here is the error:
Step 1902, time 1.902 (ps) LINCS WARNING
relative constraint deviation
On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the
Hi,
I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting i
>
> 2. MOPAC gromacs mdreun error (vidhya sankar)
It seems that you are trying to run with multiple threads. Use mdrun -nt 1 to
use only a single thread.
Gerrit
> Dear gmx users
>
> i have successfuly installed Mopac gromacs/interface. but when i run
> the QM/MM in mdr
22 matches
Mail list logo