Dear gmx-users, Mark and Justin,
thank you for your previous and precious support, but now I have another
doubt. As I told you previously, looking at my trajectory I can see that the
protein is still not fully equilibrated, then I would like to continue the
simulation. However, now if I use tpbcon
On 4/29/2011 6:45 PM, Anna Marabotti wrote:
Dear gmx-users, Mark and Justin,
thank you for your previous and precious support, but now I have another
doubt. As I told you previously, looking at my trajectory I can see that the
protein is still not fully equilibrated, then I would like to contin
Hi all,
I'm trying to use this tool with the following command (selecting the
backbone atoms: 366 atoms in total)
g_rmsdist -s 1.pdb -f traj_fit.trr -rms
But the programs stop with the following error:
Program g_rmsdist, VERSION 4.5.4
Source code file: matio.c, line: 953
Fatal error:
hi (-100
On 2011-04-29 16.32, Andrea Carotti wrote:
Hi all,
I'm trying to use this tool with the following command (selecting the
backbone atoms: 366 atoms in total)
g_rmsdist -s 1.pdb -f traj_fit.trr -rms
But the programs stop with the following error:
Program g_rmsdist, VERSION 4.5.4
Source code file:
Hi everybody,
I just ran a number of simulations with two large and roughly spherical
molecules
in a primitive model electrolyte (epsilon=80), they are constrained to the
z-axes and
i calculate the PMF using the pull code restraining the distance between the
two molecules. integration is done
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot
of troubles. But, finally I managed to solve it so maybe my
experiences can be helpful for you:
I think you should use SHAKE instead of LINC
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
Citando David van der Spoel :
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my expe
thanks felix
you are right.both exist.but how can i tell gromacs to put MG ions in the
standard vicinity of ATP? or maybe gromacs knows it already and i have to just
type "MG-ATP" instead of "ADP"?
From: "Rausch, Felix"
To: Discussion list for GROMACS users
Sajad Ahrari wrote:
thanks felix
you are right.both exist.but how can i tell gromacs to put MG ions in
the standard vicinity of ATP? or maybe gromacs knows it already and i
have to just type "MG-ATP" instead of "ADP"?
If all residues, including ligands and cofactors, exist in the .rtp dat
Thank you Mark for your response,
In carrying out the test you recommended I realised that I had set the
integrator to sd, in such a case the tcoupl parameter is ignored. This explains
my well behave temperature in the absence of setting a tcoupl option. When I
wrote the input file original
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I read the
manual section 4.7 as well. But, unfortunately, for a 5-site tetrahedral
geometry I was not able to figure out the right vsite type I should use. So, I
was wondering whether you can provide some input on the
On 2011-04-29 19.15, gyorgy.han...@fc.up.pt wrote:
Citando David van der Spoel :
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles.
Hi Gromacs users & developers,
If I modified gromacs, will my modification works if I complied it with
OPENMM and use GPU?
Thanks!
Regards,
Chi-cheng
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Chi-cheng Chiu wrote:
Hi Gromacs users & developers,
If I modified gromacs, will my modification works if I complied it with
OPENMM and use GPU?
Presumably, if you have written sound code that uses compatible functions that
are actually implemented in the OpenMM library, then yes. If you
Hi Justin,
Thanks for the reply. The part I modified is the implicit solvent
part, particularly the Still model. Also I modified a part of nonbonded
kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM
using customGBforce?
Is there a guide of how currently GROMACS is linked to OPE
Chi-cheng Chiu wrote:
Hi Justin,
Thanks for the reply. The part I modified is the implicit solvent
part, particularly the Still model. Also I modified a part of nonbonded
kernel, not sse ones. So I assumed I have to link GROMACS with OPENMM
using customGBforce?
In order to use any of the
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whe
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whe
Dear experts,
I have successfully installed a normal gromacs 4.5.4 installation on one of
my machines.
I have read the Installation Instructions that "As of GROMACS 4.5, threading
is supported, so for e.g multi-core workstations, MPI is no longer
required."
Does this mean that there is no longer
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps
I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560, max 72.359520 (between atoms 314 and 315)
bo
Sir,
I am trying to create an ionic-liquid system comprising of
1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have
generated the system using following command:
genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o
Hi Ivan
If in my system there are some of the other components such
SDS surfactant and one of these polarizable models can I use forcefield
parameters from PRODRG or not.
If no, would you please tell me about the references that I can find some
other components in polarizable water model
force fi
Hi Ivan
In which force field can I find the polarizable water models you said in
section "b" of your reply
Thanks alot
Regards
Saly
On Wed, Apr 27, 2011 at 2:30 PM, wrote:
> Send gmx-users mailing list submissions to
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Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
Thanks alot
Saly
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