Paymon Pirzadeh wrote:
One more point:
when I run the job interactively, although it works but date and time
are wrong!
step 0
step 100, will finish Wed Sep 16 16:16:00 2009
step 200, will finish Wed Sep 16 14:32:34 2009
step 300, will finish Wed Sep 16 13:57:51 2009
step 400, will finish Wed Se
Hi,
I have compiled gromacs 4.0.5 on our mac cluster (64bit) using openmpi
1.3.3 and gcc 4.2.1.
No my problem is grompp. When I manually run grompp it runs smoothly,
but when I run it as part of a job to our cluster it crashes:
/var/spool/torque/mom_priv/jobs/ ... .SC: line 27: 91546 Segmentatio
Dear Gromaxs users
I want to plot a graph from a remote computer. My operating system is windows
Vista. I connect to Imperial college in London via VPN connection. There I do
the simulations using gromacs. Now I want to plot for example the density.xvg
using gnuplot, but I get this error:X conne
On Aug 27, 2009, at 2:51 PM, sunny mishra wrote:
Dear all,
I was earlier facing problem regarding the mismatch of atoms in .top
and .gro file and then after useful discussion here I figured out
that some atoms were missing in my cg.pdb file and that problem is
because of the OLDER atom2c
Yeah I agree wiht you but I tested another protein as well 1BL8 to check if
there was a problem specifically in 1K4C. Even after testing 1BL8 it gives
me the same error. What do you think?
On Thu, Aug 27, 2009 at 4:11 PM, Justin A. Lemkul wrote:
>
>
> sunny mishra wrote:
>
>> Dear all,
>>
>> I w
How is it that the date and time is wrong? It is simply telling you
that the simulation will be completed on Sep 16, using the time on the
computer that the program is running on.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash Unive
Hi,
I have compiled gromacs 4.0.5 on our mac cluster (64bit) using openmpi
1.3.3 and gcc 4.2.1.
No my problem is grompp. When I manually run grompp it runs smoothly,
but when I run it as part of a job to our cluster it crashes:
/var/spool/torque/mom_priv/jobs/ ... .SC: line 27: 91546 Segm
Hi Justin,
"There is something physically unrealistic about your model"
You are right!
The main problem I found out is that some of the structures in my
Solution broke down..
I used ...
genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top
-XX.gro
To generate mult
Vitaly V. Chaban wrote:
Then I believe you have problems with MPI.
Before I experienced something alike on our old system - serial
version worked OK but parallel one failed. The same issue was with
CPMD by the way. Another programs worked fine. I didn't correct that
problem...
On Thu, Aug 27, 2
Is there a correct way to obtain the standard deviation for these data sets?
> >
> > Ragnarok sdf wrote:
> > > When analysing FEP simulations. After running g_energy -f fep000.edr
> -f2
> > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I
> > tried
> > > to obtain the stand
Hi GROMACS users
Does anyone have any information on the simulation of gold nanoparticles with
GROMACS?
Thank you in advance
George
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
I don't understand what you want exactly.
Your g_energy command does exponential averaging, that happens
on the printed data points. So there g_analyze or any program will do fine.
For the original data g_energy gives the exact standard deviation
over all MD steps, called RMSD.
But do you really
Hi,
I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I
have to run the GROMACS in double precision .For this i went through the
manual and made necessart changes in .mdp file.But when I gave grompp_d it
showed like this
[abhi...@scfbioserver 1omb]$ grompp_d -v -f em.mdp -c b4e
Hi GROMACS users
Does anyone have any information on the simulation of gold nanoparticles with
GROMACS?
Thank you in advance
George
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
Dear gmx developer,
I have read the paper* " An Improved United Atom Force Field for Simulation
of Mixed Lipid Bilayers " J. Phys. Chem. B 2748 2009, 113, 2748–2763*
Is the new force field (43A1-S3) can instead of the FF of Berger et al. for
lipid simulations? When will it be incorporated in t
lammps lammps wrote:
Dear gmx developer,
I have read the paper/ " An Improved United Atom Force Field for
Simulation of Mixed Lipid Bilayers " J. Phys. Chem. B 2748 2009, 113,
2748–2763/
Is the new force field (43A1-S3) can instead of the FF of Berger et al.
for lipid simulations? When
Hi,
I used the followng command and encountered an error. Can someone please
offer a solution.
grompp -f grompp.mdp -n index.ndx -p topl.top -c conf.gro -o water.tpr
:-) G R O M A C S (-:
Green Red Orange Magenta Azure Cyan Skyblue
No information on what you requested, but I do have some tips on how
to get help from a mailing list. Please understand that I'm sending
this only to try to help you.
Don't use all caps. Don't double post, we saw the first one. Show us
that you have done some work and, if possible, approach
--- On Fri, 8/28/09, delara aghaie wrote:
From: delara aghaie
Subject: [gmx-users] question
To: gmx-users@gromacs.org
Date: Friday, August 28, 2009, 2:17 AM
Dear Gromaxs users
I want to plot a graph from a remote computer. My operating system is windows
Vista. I connect to Imperial co
I am terribly sorry. I have not expressed myself well. I meant the standard
error of the mean energy given by g_energy. So I believe I would like to
know the standard error estimate.
>
> I don't understand what you want exactly.
> Your g_energy command does exponential averaging, that happens
> on
Hi,
I'm trying to continue a sim using:
old cmd line + -cpi state.cpt -append yes
where old cmd line =
mpirun -np 1 $GROMACS_T37/mdrun -s shear -c shear_final -g shear_final
-o shear
All files exist.
and I get:
---
Program mdrun, VERSION 4.0
simon sangma wrote:
---
Program grompp, VERSION 4.0.4
Source code file: readir.c, line: 1058
Fatal error:
Atom 1 in multiple T-Coupling groups (1 and 2)
---
The error message is quite cle
delara aghaie wrote:
--- On *Fri, 8/28/09, delara aghaie //* wrote:
From: delara aghaie
Subject: [gmx-users] question
To: gmx-users@gromacs.org
Date: Friday, August 28, 2009, 2:17 AM
Dear Gromaxs users
I want to plot a graph from a remote computer. My operating sys
Hi,
-append yes is incorrect, it should be -append without the yes.
In this case this error has no effect though.
Is your trr file larger than 2 GB?
We have fixed a bug with this in the upcoming 4.0.6 release.
Berk
> Date: Fri, 28 Aug 2009 16:48:07 +0200
> From: alexander.h...@mytum.de
> To: g
Hi,
I am trying to set up a simulations of short peptides in water, and I
want to eliminate the electrostatic interactions of the N-terminal
amino group and the C-terminal carboxyl group by capping them, with
acetate for the N-terminus and a C-terminal amide.
I built the PDB file
Warren Gallin wrote:
Hi,
I am trying to set up a simulations of short peptides in water, and
I want to eliminate the electrostatic interactions of the N-terminal
amino group and the C-terminal carboxyl group by capping them, with
acetate for the N-terminus and a C-terminal amide.
Hi,
It looks like the wiki site (oldwiki) is not working, and perhaps has been that
way for several days, when I last tried to access it.
I was able to look up some stuff on the WIKI-Import feature of the new site, but
all the links within the articles point to wiki.gromacs.org, which has no
Justin A. Lemkul wrote:
Hi,
It looks like the wiki site (oldwiki) is not working, and perhaps has
been that way for several days, when I last tried to access it.
I was able to look up some stuff on the WIKI-Import feature of the new
site, but all the links within the articles point to wiki.
Hi George,
I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?
~ Vitaly
>
> Hi GROMACS users
>
> Does anyone have any information on the simulation of gold nanoparticles with
> GROMACS?
>
> Thank you in advance
>
> George
_
There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for MD run, then I run into
th
Payman Pirzadeh wrote:
There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for
Dear all,
At the final step of my mdrun I get LINCS warning. I don't know whats the
issue. Please help me out.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 51.050964, max 314.598846 (between atoms 3 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom
Hi,
I just installed v. 4.0.5
Wen I ran the gmxtests I got the following output:
All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Ch
sunny mishra wrote:
Dear all,
At the final step of my mdrun I get LINCS warning. I don't know whats
the issue. Please help me out.
If I had a nickel for every time I saw a LINCS warning on this list... :)
The answer is always the same. There is something physically unrealistic about
y
Which test set are you using? These failures are to be expected for earlier
versions in the 4.0.x series, but were fixed in a 4.0.5-compatible version. I
don't believe these failures ever indicated anything truly wrong, but the newest
version has different (clearer and more detailed) output
Hi Vitaly
I 've searched in the Web of Science for gold nanoparticles and Gromacs but
I didn't get any results. Could you give me some more details on these
publications?
Are they performed with GROMACS? Which forcefield has been used?
Thank you in advance
George
- Original Message ---
George Tsigaridas wrote:
Hi Vitaly
I 've searched in the Web of Science for gold nanoparticles and Gromacs
but I didn't get any results. Could you give me some more details on
these publications?
If you don't find what you want, keep searching. For example, a search in WoS
for "gold nano
Thank you Justin. A very interesting paper. Next time, if I want to search
for something I 'll call you ... :)
Thanks again
George
- Original Message -
From: "Justin A. Lemkul"
To: "Discussion list for GROMACS users"
Sent: Saturday, August 29, 2009 1:30 AM
Subject: Re: [gmx-users]
Warren Gallin wrote:
I could only find the 4.0.4 tests, which are what I ran.
Where would I find the latest tests?
It used to be linked from the wiki, but the site is still down and I can't find
it on the main page. I imagine you could pull down the latest development
version (which shou
I could only find the 4.0.4 tests, which are what I ran.
Where would I find the latest tests?
Warren Gallin
On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote:
Which test set are you using? These failures are to be expected for
earlier versions in the 4.0.x series, but were fixed in a 4.0.5
I am terribly sorry. I have not expressed myself well. I meant the standard
error of the mean energy given by g_energy. So I believe I would like to
know the standard error estimate.
>
> I don't understand what you want exactly.
> Your g_energy command does exponential averaging, that happens
> on
Ragnarok sdf wrote:
I am terribly sorry. I have not expressed myself well. I meant the
standard error of the mean energy given by g_energy. So I believe I
would like to know the standard error estimate.
Based on the output RMSD (standard deviation), it seems rather straightforward
to cal
abhijit kayal wrote:
Hi,
I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I
have to run the GROMACS in double precision .For this i went through the
manual and made necessart changes in .mdp file.But when I gave grompp_d
it showed like this
[abhi...@scfbioserver 1omb]$
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