Dear Mark,
I basically rerun a simulation, both in xtc and trr
format,
using slightly different tpr file, varying the gro file
used to construct it, and different gmx version, 3.2 and
3.3. From those rerun I extracted and compared the bonded
and non-bonded energies.
The most stricking is that
Dongsheng Zhang wrote:
Dear All,
I want to run gromacs in supercomputer center at my school. When I used
pdb2gmx, it gave me an error message as follows:
illegal instruction (core dumped out)
Could anyone give a clue what's happening? Thank you in advance.
We've got about as much chance of gu
Dear All,
I want to run gromacs in supercomputer center at my school. When I used
pdb2gmx, it gave me an error message as follows:
illegal instruction (core dumped out)
Could anyone give a clue what's happening? Thank you in advance.
Dongsheng
___
gmx
Xavier Periole wrote:
The energies indicate that:
0) I see a systematic difference with the original energies (not
significant), but using
the trr file helps getting better.
1) I do not see ANY difference between the rerun using the two tpr file
(Unexpected ?!?!)
2) I do not see significant
Joanne Hanna wrote:
Hi
Can anyone please help! I have been trying to compile gmx 3.1.4 on pcs running
fedora core 3 and 4 however I get a range of warnings during the make stage.
Unless you absolutely need back-compatibility of gromacs version for
some reason, you'd be well advised to get a
By the way, for the optimal setup of molecluar dynamics, there are some difference for gromacs and gromos, such as in the mdp file, GROMOS 96 force field uses nstlist = 5 and rvdw = 1.4.
Can anyone give me a standard mdp file to do MD simulation with gromacs package using gromos96 force field?
Dear users:
Maybe, this is a stupid question, but I really have no concepts about other
kinds of boundary conditions except for pbc.
Anybody know how many or which boundary condition is used in GMX except for
pbc, and how to set the parameters in the input files?
Because I wanna make a com
My pull.ppa file is as follows.
verbose = noruntype = afmgroup_1 = pull_1group_2 = pull_2reference_group = pp_flateweights_1 = 55.847 reference_weights = 14.0067 14.0067 14.0067 14.0067weights_2 = 14.0067 1.008 12.011 12.011 12.011 14.0067 1.008 12.011 12.011 14.0067 12.011 15.9994reftype = comre
Dear All,
I use gromacs version 3.3 to perform a simulation on a protein-drug complex. I chose the gromos96 53a6 force field. But how to generate the parameter file of the drug fo gromos96 53a6 force field. The Dundee PRODRG server produce files in format of gromacs/gromos87.
But the produce fil
How is pbc handled in calculating structure factors (SF) from MD
simulation in general? I wrote a small program to compute SF for a box
of water given the trajectory obtained from Gromacs, but it suffers
from an edge effect (hard-sphere scattering).
Do people (or does Gromacs) calculate radial dis
Ack, nothing like an announcement to turn up a new bug. There's one
now in trjconv but pdb2gmx is still ok. If you try this
after you unpack just copy gmx_trjconv.c.dist onto gmx_trjconv.c
and you'll still have the original trjconv program.
Regards,
David Mathog
[EMAIL PROTECTED]
Manager, Seque
I've been working on table driven translation between PDB
and AMBER/GROMACS "PDB" files. That is, getting things that are
nominally in PDB format into, through, and out of the GROMACS package
without having to edit PDB files. Especially structures that used
DNA and Protein, and so had to use the
Hi
Can anyone please help! I have been trying to compile gmx 3.1.4 on pcs running
fedora core 3 and 4 however I get a range of warnings during the make stage.
For fedora 4 the warnings are;
pme.c: In function 'solve_pme':
pme.c:306: warning: dereferencing type-punned pointer will break
strict-al
Hello
I have encountered warning messages when compiling on computers running either
fedora core 3 or 4 which run gcc v 3.4 and v 4.0 respectively.
I have however succesfully compiled the same version of gmx 3.2.1 from the
source code on machines running v 7.3 redhat which uses gcc v 2.96.
The w
Dear all,
sorry for the long message.
I am simulating the hydrophobic interaction between
two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent
with all-bonds constraints (LINCS) by GROMACS 3.3 downloaded from GROMACS
web-site.
In order to allow them to interact I
Hi,
I fixed this problem on my login node on the cluster I'm using by getting the
libXm.so.3 file from another machine and copying it to
/home/bruce/lib/libXm.so.3. After that I could run GROMACS without
re-compiling. (At least it stops the complaints about the missing library and
lets you run jo
I forgot the energy file. It is now attached.
XAvier
--
--
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-
Dears,
I have reruning simulations using gmx3.2 and found out some deferences
between the original and rerun energies. I found the posts made by David
Mobley and Mickael Shirts about this issue. Accordingly I downloaded
gmx3.3 and compiled it with the fixed md.c for the rerun, found in the
bugzi
Check your Linux's rpm resipository for a package containing this file.
The best way of avoiding this could be using -without-x for Gromacs'
configure.
Yang Ye
Rongliang Wu wrote:
> hello all,
> i've got a problem whem i intend to run a parallel mdrun, when i met with
> such error:
>
> error w
I succeeded mdrun with one pulling group, but I got the error message with two pulling groups like these.
Error 1[file, line1]
Unknown left-hand ‘group_2’ in parameter file.
Error 2[file, line1]
Unknown left-hand ‘weights_2’ in parameter file
Error 3[file, line1]
Unknown left-hand ‘afm_k2’ i
Hi,
Sounds like you compiled on a frontend that has X11 installed, but
the nodes you are running on don't.
X11 is usually only available as a dynamic library (i.e., you can't
compile it statically), so disable X11 support instead with
./configure --without-x (+ your current options)
Chee
Hi,
Is it possible to send a pdf to this email?
Thanks, D.L.Lynch
>>> [EMAIL PROTECTED] 03/20/06 5:58 AM >>>
Andrea Carotti a écrit :
> Thank you for the fast answer.
> Please let me (us) know, when it will be fixed.
> Thanks
> Andrea
I did a cvs manual as of february 2nd, 2006.
If you are int
hello all,
i've got a problem whem i intend to run a parallel mdrun, when i met with such
error:
error while loading shared libraries: libXm.so.3: cannot open shared object
file: No such file or directory
what's the problem and mpi is LAM
--
Ronglia
Andrea Carotti a écrit :
Thank you for the fast answer.
Please let me (us) know, when it will be fixed.
Thanks
Andrea
I did a cvs manual as of february 2nd, 2006.
If you are interested in the PDF, let me know, i'll send you.
Regards,
Stéphane
--
Stéphane Téletchéa, PhD. htt
Hi Raja,If you have the average structure and the reference, you can use g_confrms to fit them and obtain the rms value. In addition you might want to try the fitting routine (align) in PyMol (
pymol.sourceforge.net), which can omit outliers.Cheers,TsjerkOn 3/20/06, raja <[EMAIL PROTECTED]
> wrote:
Thanks for the kindly replies.
I write a python script to remove the water and then substitute the ion with
TMA, Then add water again.
If I only add several TMA, It work well. Otherwise, the box have to enlarged,
since the atoms went out of the box.
Then I find -ci option of the genbox may be w
Dear GMXIONs,
How to find out RMSD value between two RNA structures in
GROMACS ? I want to compare the crystal structure of the RNA
of my interst with the average structure of RNA after
simulation. Swisspdb viewer not helpful for this case.
With thanks
Dear GMX users,
I am interested in doing Simulated Annealing
MD using GROMACS. Does any body have any tutorial
or protocol for doing?
With thanks
Dr.C.Karunakaran
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