Dear gmx_users,
I am working on lipid/drug molecule system.
I could make the ligand topology by PRODRG and get DMPC.itp from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies.
To add ligand molecule I first changed its coordinate by:
editconf -f drg.gro -o drg_newbox.gro -c
Dear GMX users,
Recently, I want to caculate the free energy for K+-NA+ in bulk with
GMX4.5.4 using charmm 27 force field. I change ion.itp
[ moleculetype ]
; molname nrexcl
K 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 POT 1 K K 1
You can put whichever spin you like into what is said, but there is a clear
(and unnecessary) fault with the way coordinates are stored in gro files
when made from pdb using pdb2gmx.
On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/11/2011 5:07 AM, Igor Druz
My my. Why is it a fault to adhere to ISO units (nm) over non-standard
(A)? It's a choice, but a choice is not faulty. The consequences may
be undesirable. But shouldn't a user, certainly a computation
scientist, understand the file formats, as an experimentalist should
know its solvent? And know
You are missing the point. Quoting my response to David:
I appreciate the history of the matter, but it would save a lot of headache
to store coordinates in angstroms in gro files, i.e., not to omit 2 in
4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What
is the point in
Hi Igor,
Please do read the manual. The GRO file format is a fixed-width format
with %8.3f for coordinates, velocities and forces. Changing the format
to %9.4f will break everything written in fortran. And, yes, people
still use fortran. So which point did I miss? :)
Cheers,
Tsjerk
On Sun,
write to gro in angstroms, read from gro in angstroms, convert into nm in
grompp.
On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Igor,
Please do read the manual. The GRO file format is a fixed-width format
with %8.3f for coordinates, velocities and forces.
On 2011-11-27 12:15, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm
in grompp.
once more you don't have to use gro, use g96 if precision is important.
if we'd introduce a gro format in angstrom it couldn't be called .gro
anyway since that would confuse
On 27/11/2011 10:15 PM, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm
in grompp.
What are you trying to communicate with this hypothetical workflow?
Historical file formats imply particular units and are often limited to
a particular precision.
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants that make 10 micelle. I want to
compute rdf for surfactant relative to the center of mass of micelle.
When I do g_rdf, the program ask me 2 groups that the first one is COM, but it
is COM of molecules that I
On 2011-11-27 12:27, mohammad agha wrote:
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants that make 10 micelle. I want to
compute rdf for surfactant relative to the center of mass of micelle.
When I do g_rdf, the program ask me 2 groups that the first one is
On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/11/2011 10:15 PM, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm in
grompp.
What are you trying to communicate with this hypothetical workflow?
Historical file
Back to square one! The point you are missing is that 4.172 A is not
equal to 0.417 nm and pdb2gmx does it without any warning.
You have a point. It is not possible to change the file formats without
creating great havoc as I'm sure you understand, but a warning that
precision is lost
On 27/11/2011 7:23 PM, parto haghighi wrote:
Dear gmx_users,
I am working on lipid/drug molecule system.
I could make the ligand topology by PRODRG and get DMPC.itp from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies.
To add ligand molecule I first changed its
Hi Chris, Druz
Thank you very much for your reply. Indeed I have read several papers where the
diffusion of water at the membrane surface have been computed. Since the
diffusion of the interfacial water is an useful properties to examine the
micelle/surface irregularities, I would hope that
Well, the positive way of looking at this is that it appears that
nobody has ever done it before. If somebody has done it (in charmm for
instance) then you might be able to convert the format of your .xtc
and use their tools to analyze it.
Good luck,
Chris.
-- original message --
Thank
Dear All,
Is there a way to let GROMACS to calculate and write the total dipole moment
on-the-fly?
I realize that g_dipoles can be used to calculate the total dipole moment
using a stored trajectory. However, for a large system it is not very
feasible to write the trajectory at a
On 11/27/11 3:26 PM, Dr. Vitaly V. Chaban wrote:
Dear All,
Is there a way to let GROMACS to calculate and write the total dipole moment
on-the-fly?
I realize that g_dipoles can be used to calculate the total dipole moment using
a stored trajectory. However, for a large system it is not very
Dear Dr.Abraham,
Thanks a lot for your response.
I have another question. Should I add several molecules in DMPC together or
I should add them one by one?
Best regard
Parto
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the
Hi,
I don't remember any incident related to tools crashing, but I do
recall a problem which initially was attributed to a known gcc 4.1 bug
(http://redmine.gromacs.org/issues/431), but it turned out to be a GB
bug.
However, knowing that there is such a nasty bug in gcc 4.1, we thought
it's
Hi Andrzej,
GROMACS 4.6 is work in progress, it will have native CUDA acceleration
with multi-GPU support along a few other improvements. You can expect
a speedup in the ballpark of 3x. We will soon have the code available
for testing.
I'm a little skeptical about the 5x of ACEMD. What setting
Random hijack:
Will the CUDA acceleration support CMAP or will it still be limited to
the limitations of OpenMM that it currently has?
On 2011-11-27 12:10:47PM -0600, Szilárd Páll wrote:
Hi Andrzej,
GROMACS 4.6 is work in progress, it will have native CUDA acceleration
with multi-GPU
Native acceleration = not relying on external libraries. ;)
--
Szilárd
On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai p...@uab.edu wrote:
Random hijack:
Will the CUDA acceleration support CMAP or will it still be limited to
the limitations of OpenMM that it currently has?
On 2011-11-27
Dear GMX user,
Can anyone suggest how to use simulated a protein-ligand complex using
AMBER force field in GROMACS.
And one thing more in another simulation i am trying to find out the
difference in protein complex interaction by mutating one residue. Right
now I am using simple procedure
Oh cool. Looking forward to it then!
On 2011-11-27 02:50:43PM -0600, Szilárd Páll wrote:
Native acceleration = not relying on external libraries. ;)
--
Szilárd
On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai p...@uab.edu wrote:
Random hijack:
Will the CUDA acceleration support
Rohit Farmer wrote:
Dear GMX user,
Can anyone suggest how to use simulated a protein-ligand complex using
AMBER force field in GROMACS.
Though the force field is different, the workflow is the same as:
Hi!
Will it use CUDA or OpenCL? Second one will be more common since it
will work with wider range of platfroms (cpu, gpu, fcpga)
Szilárd Páll писал 27.11.2011 23:50:
Native acceleration = not relying on external libraries. ;)
--
Szilárd
On Sun, Nov 27, 2011 at 9:33 PM, Peter C. Lai
Is the total dipole moment stored in the energy file of Gromacs 3.3 correct?
Thanks.
Hao
-Original Message-
From: David van der Spoel
Sent: Sunday, November 27, 2011 9:36 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: gmx-users Dipole
On 11/27/11 3:26 PM, Dr.
dear teacher,
when i do remd in the npt ensemble.
REMD: NPT -replex 4000
dt= 0.0001
step 172000, will finish Sat Dec 31 18:44:12 2011
---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549
Range checking error:
杜波 wrote:
dear teacher,
when i do remd in the npt ensemble.
REMD: NPT -replex 4000
dt= 0.0001
step 172000, will finish Sat Dec 31 18:44:12 2011
---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549
Range
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