Message: 1
Date: Tue, 11 Oct 2011 22:05:27 +0200
From: Szil?rd P?ll
Subject: Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset=ISO-8859-1
Hi Gregory,
I am not very familiar with the could computing offerings
Thank you Mark for your answer!
I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundreds bar.
What I found very strange was the i
Dear all,
any other suggestions on how to operate with g_hbond in order to allow
convergence of the autocorrelation function (see message below)?
Moreover, I have another question. On the same trajectories, I'm using
g_hbonds also to infer the contacts between the protein and the ligand (and
poss
On 12/10/2011 8:04 PM, Nuno Azoia wrote:
Thank you Mark for your answer!
I agree with you when you say that the high pressure is not itself a
problem. To avoid that problem I change my system from 1000 molecules
to 27000 molecules, and the pressure change from several thousands to
several hundre
Dear Gromacs Users,
I am trying to study the free energy of binding in a protein-ligand complex.
I use the following pull input in my mdp file:
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N Y N
pull_start = yes
pull_ngroups = 1
pul
I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
time, and using 4.0 I get almost 500 after 1n
Dear Stephan,
> Radeons work as well. You can put a 3-4 GPU board together with the highest
> end AMD or Intel chip for 3K, plus 16G RAM if you look around for a day or
> two, but the cooling is the main problem (with 1/4 the price radeons Vs. GTI
> cards), so one has to take cooling into acco
Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and randomly inside a
system which is going to be solvated in spc216 water. I used genbox command
to add the correct number of water molecules needed to solvate the box. The
drug molecules are located very closed
I was recently told in passing that it would be possible to construct a
'potential energy landscape' from the simulations I have performed. This way I
could remove any loading rate differences between simulations and experimental
force experiments I've been performing ... however I cannot find
Hello Michael or others,
It seems I'm still getting errors when doing a FEP on a molecule (a
-CH3 to a -H). This below is for when I was charging things from a -H
uncharged to -H charged, although it also happens when I'm actually
converting the -CH3 to -H (at Lambdas greater than 85%). I made s
meisam valizadeh kiamahalleh wrote:
Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and
randomly inside a system which is going to be solvated in spc216 water.
I used genbox command to add the correct number of water molecules
needed to solvate the box.
>From the Gromacs on GPU page
(http://www.gromacs.org/Downloads/Installation_Instructions/GPUs)
These are the compatible GPU cards (Basically buy NVidia for now):
v2.0
Compatible NVIDIA CUDA versions (also see OpenMM version compatibility above):
v3.x
Compatible hardware (for details consult the
Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water r
Dear Markus,
If you know the residues composing the cavity (and I think you know it),
you can simply change the coordinates
of the water molecule in the .gro file to move the water in the cavity.
Francesco
Il 12/10/2011 18:17, Markus Weingarth ha scritto:
Dear Gromacs-users,
I would like t
Hi Francesco,Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory.CheersMarkusVon: "Francesco Oteri" Gesendet: Oct 12, 2011 6:41:05 PMAn: gmx-users@gromacs.orgBetreff: Re: [gmx-us
Markus Weingarth wrote:
Hi Francesco,
Thanks for your answer, but that's not an option for me. I really would
like to force the penetreation of a water-molecule into this cavity over
the couse of the trajectory.
Use the pull code.
-Justin
Cheers
Markus
Natalie Stephenson wrote:
I was recently told in passing that it would be possible to construct a
'potential energy landscape' from the simulations I have performed.
This way I could remove any loading rate differences between simulations
and experimental force experiments I've been performi
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have generated the topologies for the ligand using MKtop. The output from
the MKTOP gives the top file, but not the coordinate/structure file. Please
let me know if any tutorial is available for merging t
ram bio wrote:
Dear Gromacs Users,
I am using opls FF for my protein-ligand simulations in lipid bilayer. I
have generated the topologies for the ligand using MKtop. The output
from the MKTOP gives the top file, but not the coordinate/structure
file. Please let me know if any tutorial is a
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp; and
included the ligand.itp line in the topol.top file generated from the
pdb2gmx. During the pdb2gmx command,
Dear Justin
Thank you very much for your always prompt reply. Actually, I added many of
drug molecules by copying and pasting a single molecule in discovery studio
software. I could even move the drug molecules to any desired locations by
select and dragging them. Finally I used the output pdb fil
ram bio wrote:
Dear Justin,
Thanks for the information.
Initially, i just wanted to run a simulation of protein-ligand in water
solvent . I renamed the topology.top generated from mktop to ligand.itp;
and included the ligand.itp line in the topol.top file generated from
the pdb2gmx. During
meisam valizadeh kiamahalleh wrote:
Dear Justin
Thank you very much for your always prompt reply. Actually, I added many
of drug molecules by copying and pasting a single molecule in discovery
studio software. I could even move the drug molecules to any desired
locations by select and draggi
Dear Justin,
As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters during
md simulations in lipid bi layer. I found that MKTOP can generate topology
files using opls ff for small molecules.
I have also tried s
ram bio wrote:
Dear Justin,
As i generated the protein-ligand docked complex using opls FF, for the
consistency, i am trying to use opls ff generated ligand parameters
during md simulations in lipid bi layer. I found that MKTOP can generate
topology files using opls ff for small molecules.
Hello all,
It seems I'm still getting errors when doing a FEP on a molecule (a
-CH3 to a -H). This below is for when I was charging things from a -H
uncharged to -H charged, although it also happens when I'm actually
converting the -CH3 to -H (at Lambdas greater than 85%). I made sure
to ke
Dear Justin,
Thanks, and I accept your suggestions;
If SwissParam was designed to be used with CHARMM, the most intuitive next
step is to use CHARMM for the MD, is it not?I understand the point about
trying to keep the force fields consistent between docking and MD, but it
may not be feasible (i.
> Thanks, and I accept your suggestions;
>
> If SwissParam was designed to be used with CHARMM, the most intuitive next
> step is to use CHARMM for the MD, is it not?I understand the point about
> trying to keep the force fields consistent between docking and MD, but it
> may not be feasible (i.e.,
Did you look at atom 2073?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a
On 13/10/2011 12:35 AM, Nuno Azoia wrote:
I know that from the beginning. That's why I found very strange the
increasing on the system volume. My initial setup have a density of
~400g/L, and for liquid chloroform is ~1400g/L.
Using gromacs-4.5 I get densities of about 200 after 750ps simulation
t
On 13/10/2011 2:13 AM, meisam valizadeh kiamahalleh wrote:
Dear GMX users
Good day to you
I have some drug molecules (cisplatin) added manually and
randomly inside a system which is going to be solvated in spc216
water. I used genbox command to add the correct number of water
molecules needed
Done
2011/10/10 Mark Abraham
> On 11/10/2011 4:51 AM, César Ávila wrote:
>
> v4.5.4
> As I commented above, I had to manually add an entrance for the cmap terms
> in the topology file as pdb2gmx would not generate them for the alanine
> dipeptide. There seems to be no problem for larger peptide
ram bio wrote:
Dear Justin,
Thanks, and I accept your suggestions;
If SwissParam was designed to be used with CHARMM, the most intuitive
next step is to use CHARMM for the MD, is it not?I understand the point
about trying to keep the force fields consistent between docking and MD,
but it m
> G92/G94:
> GeForce 9800 GX2/GTX/GTX+/GT
> GeForce 9800M GT
> GeForce GTS 150, 250
> GeForce GTX 280M, 285M
> Quadro FX 4700
> Quadro Plex 2100 D4
> GT200:
> GeForce GTX 260, 270, 280, 285, 295
> Tesla C1060, S1070, M1060
> Quadro FX 4800, 5800
> Quadro CX
> Quadro Plex 2200 D2, 2200 S4
> GF1xx (F
Dear Justin,
Thanks.
The POPC bilayer i am using is with berger lipids, corrected for dihedrals
so as to be compatible with the OPLS FF for aminoacids.
While searching for the literature on compatibility of lipid FF and protein
FF, I found few references where similar modification was done for
ram bio wrote:
Dear Justin,
Thanks.
The POPC bilayer i am using is with berger lipids, corrected for
dihedrals so as to be compatible with the OPLS FF for aminoacids.
I think significantly more parameters than just dihedrals need to be altered to
make the Berger united-atom force fie
Hi Nathalia,
Right, gcc 4.1 is quite controversial as these is bug in it which is
though to be causing mdrun crashes. So you better stay away from 4.1
as well as from other old gcc versions. I'd recommend 4.5 or 4.6 as
these have gotten really good, even compared to icc - at least when it
comes to
Hi there,
I am trying to run the free energy tutorial by David mobley mentioned at *h
ttp://
www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial*
While running a test run for lambda value of 0, I found that there is some
problem with the generated trajectory, I observed the dist
All,
When I try to download Gromacs-XXX from
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz, I am getting following
error:
ISA Server: extended error message :
200 Switching to Binary mode.
200 PORT command successful. Consider using PASV.
425 Failed to establish connectio
39 matches
Mail list logo
