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Andreas Kring, Ph.D.-student
University of Copenhagen
Niels Bohr Institute
Universitetsparken 5
DK-2100 Copenhagen
Denmark
Phone
Office (D304): (+45) 35 32 04 91
Home: (+45) 77 42 55 78
Mobile:(+45) 61 77 55 78
E-mail: [EMAIL
Hello all.
I've been searching the archives with no luck so here goes:
I am using shell molecular dynamics to simulate a hydroxide ion
dissolved in water. I have been using the steepest descent minimizer
(tried in the range from 30 to 70 steps) to minimize the system,
but I'm not
2. How to run a parallel simulation with Gromacs 4.0? Are there any
special tips for a optimized parallel run? I've tried a set of runnings
but found the accelerations are not good enough as I expected.
I do something like this (for 8 CPUs):
$ grompp -c system.gro -p topology.top -f
Berk Hess skrev:
Hi,
Could you file a bugzilla report and attach the tpr file?
Please also mention at what step you get this error
(run mdrun -v to get the step numbers).
Berk
Sure, no problem.
Regards
Andreas
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Thomas Schlesier skrev:
Hi all,
does somebody know from where the default parameters for g_hbond (angle
Acceptor-Hydrogen-Donor = 30° ; distance Acceptor-Donor = 0.35nm) are?
I found nothing in the manual about that.
Maybe you can find a hint in Luzar et al., J. Chem. Phys., 98, 8160 (1993)
Hi all.
I have just installed GROMACS 4.0. My system consists of one hydroxide
ion and 999 polarizable water molecules. When the system is minimized
(using only one CPU) with a steepest descent minimizer, there are no
problems. But when I try to minimize exactly the same system using 4 or
8
Andreas Kring skrev:
Hi all.
I have just installed GROMACS 4.0. My system consists of one hydroxide
ion and 999 polarizable water molecules. When the system is minimized
(using only one CPU) with a steepest descent minimizer, there are no
problems. But when I try to minimize exactly the same
Hello all.
I have read the manual and searched the archives, but I am still a
little confused so here goes:
I am going to perform an MD simulation of a molecule consisting of 38
atoms and with a total charge of -4e (water as the solvent). For this
molecule it is not possible to make charge
David van der Spoel wrote:
Andreas Kring wrote:
Hello all.
I have read the manual and searched the archives, but I am still a
little confused so here goes:
I am going to perform an MD simulation of a molecule consisting of 38
atoms and with a total charge of -4e (water as the solvent
, 2008 at 5:59 AM, Andreas Kring [EMAIL PROTECTED] wrote:
Thank you for your reply. I tried the following:
VMD computes distances between pairs of atoms to draw a bond. So I
think your atoms are too distanced from each other.
Check the bond distribution during MD and compare with your topology.
C-CL
Thank you for your reply. I tried the following:
VMD computes distances between pairs of atoms to draw a bond. So I
think your atoms are too distanced from each other.
Check the bond distribution during MD and compare with your topology.
C-CL should be around 1.76A.
In 1,1,1-trichloroethane
Hello,
I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and
it all worked nicely. But when I try to visualize the trajectory file in
VMD some of the C-Cl bonds are missing (although all the atoms appear on
the screen - only bonds are missing)?
Can I do anything to fix
Collins Nganou skrev:
Dear Users.
Greetings. Please someone can tell me how can I proceed
to save all MD snapshot for a long time simulation
after equilibration.
You can set the parameters below to the value 1 in the configuration
file for mdrun.
nstxout = 1
nstvout = 1
nstfout = 1
Exactly what I was looking for!
Thanks a lot!
/Andreas
Justin Lemkul skrev:
Is this what you are looking for?
http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
-Justin
Andreas Kring wrote:
Hello all,
Is it somehow possible to pass arguments to g_rdf from the command
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Thanks a lot. Now everything works perfectly!
/Andreas
Hello all.
I'm trying to simulate an argon liquid. The OPLS-AA force field is used
with the files from /usr/local/gromacs/share/gromacs/top. But I get an
error when I run
$ grompp -f NVT.mdp -c Ar.gro -p Ar.top
---
Program grompp, VERSION
Justin A. Lemkul skrev:
Just thinking out loud, but maybe Argon is too long of a name for the
residues. The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example). Maybe the length of the name is throwing off the
formatting. Why don't you try again with a residue
Continuation of thread
http://www.gromacs.org/index.php?option=com_wrapperItemid=84
(answered by David van der Spoel)
Hello all,
I ran a MD simulation of TIP4P water in the NVT ensemble (976
molecules,
density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This
works out
Hello all,
I ran a MD simulation of TIP4P water in the NVT ensemble (976 molecules,
density=0.98 g/cm3, T=300K (Nose-Hoover), SETTLE and PME enabled). This
works out fine, i.e. I get a correct radial distribution function
(g_OO), but the heat capacity (C_V) is wrong. I calculated it using the
Hello all.
I'm new to Gromacs, so sorry for this (probably naive) question:
In Table 5.3 in the Gromacs manual version 3.3, the parameters for
[atomtypes] are: atom type, mass, charge, particle type, V and W.
In the Gromacs directory containing the the force fields
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