Dear all,
Could you please tell me what kind of error limit is accepted
for running NVT and NPT equilibration in terms of Temperature, Pressure and
Density.
Thank you,
With Regards,
Ravi Kumar V
IPC Dept.,
IISc, INDIA.
--
gmx-users mailing listgmx-users@gromacs.org
Ravi Kumar Venkatraman wrote:
Dear all,
Could you please tell me what kind of error limit is
accepted for running NVT and NPT equilibration in terms of Temperature,
Pressure and Density.
You should obtain the values you set as ref_t and ref_p if you've done
equilibration
Hello,
I want to simulate system with 128 ionic liquids (128 cation+128 anion).
I have made a pdb file with a single ionic liquids ion pairs.
How can I genrate 128 ion pairs using single ion pair .pdb file.
I am using Gromacs 4.0.7 version.
Thanks
Nilesh
vac.pdf
Description: Adobe
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun and
GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing that
short range vdw energy of some snapshot are very high (
Nilesh Dhumal wrote:
Hello,
I want to simulate system with 128 ionic liquids (128 cation+128 anion).
I have made a pdb file with a single ionic liquids ion pairs.
How can I genrate 128 ion pairs using single ion pair .pdb file.
You can use genconf -nbox to generate a grid of replicates,
On 11/08/2011 12:29 AM, Da-Wei Li wrote:
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun
and GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing
that short range
Dear Mark
That is my thought too.To test this possibility, I created a mdp file
without PBC and use trjconv -pbc nojump to make whole protein. From
visualization in UCSF Chimera, the trajectory looks fine. But I still have
some snapshot that have very high vdw energy.
best
dawei
On Wed, Aug
On 10/08/2011 4:58 AM, Anthony Cruz Balberdi wrote:
Dear User:
I compiled GROMACS with OPEN64 without problems, Now I want to compile
it using the ACML libraries to compare the performance
mdrun will be identical. Several tools would improve.
How I can compile gromacs using the ACML
I want to simulate system with 128 ionic liquids (128 cation+128 anion).
I have made a pdb file with a single ionic liquids ion pairs.
How can I genrate 128 ion pairs using single ion pair .pdb file.
GENCONF
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester,
On 11/08/2011 1:18 AM, Da-Wei Li wrote:
Dear Mark
That is my thought too.To test this possibility, I created a mdp file
without PBC and use trjconv -pbc nojump to make whole protein. From
visualization in UCSF Chimera, the trajectory looks fine. But I still
have some snapshot that have very
Dear all,
we are trying to simulate molecule in specified depth in octanol to
calculate logP.
for this purpose we have used box with slab of octanol, molecule in
specified distance in z-axis and this mdp:
integrator = md
dt = 0.002
tinit = 0
nsteps = 5125000
Dear Mark
Could you please help me out? I can send you the trajectory (1000 snapshot
in pdb format), mdp, topol file. I use Gromacs-4.5.3.
I checked the pdb file in UCSF Chimera and didn't find any crash. I have
about 10 snapshot that has high vdw energy.
best,
dawei
On Wed, Aug 10, 2011
Krapnik wrote:
Dear all,
we are trying to simulate molecule in specified depth in octanol to
calculate logP.
for this purpose we have used box with slab of octanol, molecule in
specified distance in z-axis and this mdp:
integrator = md
dt = 0.002
tinit = 0
I agree that Justin is probably correct, although constraints should
technically work just fine with a highly dynamic reference group. Any
problems should show up as the system blowing up, but not in correctly
setting the position. I think that the problems can arise, however,
when you
Hello,
I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and
I need to extend them.
I have tried to use the option append like in Gromacs 4.0, using:
mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn
Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append
Rebeca García Fandiño wrote:
Hello,
I have some old calculations (Umbrella Sampling) carried with Gromacs
3.3.3 and I need to extend them.
I have tried to use the option append like in Gromacs 4.0, using:
mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn
Cl-2.4750.ndx
Thanks a lot for your quick answer!
Best wishes,
Rebeca.
Date: Wed, 10 Aug 2011 14:34:42 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] append files in Gromacs 3.3
Rebeca García Fandiño wrote:
Hello,
I have some old calculations (Umbrella Sampling)
Hi,
When running simulations at a constant higher temperatures (such as
simulating a thermophile) would changing ref_t and gen_temp to the
appropriate kelvin is enough?
Thanks and Regards,
Raghu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Hello,After undergoing a fresh installation of Gromacs 4.5.4, I still can't seem to get the mdrun-gpu program to compile and install. In order to get the original package to install I had to use the standard automake method (cmake kept getting stuck at the 'make' phase).I have managed to get an
Yes, that will be enough.
Andreas
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Ragothaman Yennamalli [ragotha...@gmail.com]
Sent: 10 August 2011 20:35
To: Discussion list for GROMACS users
Subject: [gmx-users] running
Dear Gromacs Users,
I am trying to learn viscosity calculations using non-equilibrium
method in Gromacs 4.5.4. I have gone through Hess paper and several
posts on viscosity calculation.
I have setup a system of pure water (32000 molecules) and run till 10 ns
using NPT and setting
1. NOTE 1 above suggests that I use vdwtype = Shift. When I do this, do
you recommend that I apply long range dispersion corrections for both energy
and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr
= Ener? Typically, for various (non-NVE) calculations, I have been
Hi there,
I'm trying to find the kinetic energy for a single molecule in the system.
I generated one individual group for the molecule in index.ndx file, and also
put energygrps = ** (** is the name of the group represented the single
molecule) in the .mdp file. But g_energy only allowed me to
Size Zheng wrote:
Hi there,
I'm trying to find the kinetic energy for a single molecule in the system.
I generated one individual group for the molecule in index.ndx file, and also
put energygrps = ** (** is the name of the group represented the single
molecule) in the .mdp file. But
Hi all,
In addition to modifying atomic charges to the .itp file generated by
PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4
LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ
interactions) with the vdw C12 and C6 parameters I prefer.
So should
Yun Shi wrote:
Hi all,
In addition to modifying atomic charges to the .itp file generated by
PRODRG, I also want to change the vdw C12 and C6 parameters of selected
1-4 LJ interactions and modify some 1-5 LJ interactions (or any
non-bonded LJ interactions) with the vdw C12 and C6
Hello Friends,
I would like to do simulation of a protein containing
'selenomethionine' [MSE] in coordinate file, during the first step of
pdb2gmx this residue is not recognizing by any of the force field and
getting fatal error 'Residue 'MSE' not found in residue topology
database'.
Please help
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