Justin is correct the benchmark is not necessarily what you want to
reproduce or use one of the setups used. Then 1 steps in 10 mn
that gets you 10 ps/10 mn, so 10*6*24=1,440 ps/day, depending on your
system this might actually be fine.
You use SD, I am not sure this will result in the same
Hello,I want to use spc216.gro and apply the tip3p.itp
parameters, but it would make a mistake for the pre-processor "grompp" ,it said
can't find HW atomtypes, the force file which I used is "ffG43a1.itp". my
tip3p.itp file is as follows:
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
;
If you get this to work, you may still have problems as SPC and TIP3P
have different geometries. A box of 216 waters is pretty easy to
equilibrate; you could have this done for TIP3P in no time at all.
On Apr 16, 2010, at 4:46 AM, kecy...@sina.com wrote:
Hello,I want to use spc216.gro an
Hello,
I have a question regarding the dihedral section in a topology file. If I
define two parameters sets for the same dihedral, are the energies added up or
is the first one replaced by the second one ? Unfortunately there is no
sentence in the manual regarding this.
Cheers,
Flo
--
Flor
On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote:
Hello,
I have a question regarding the dihedral section in a topology
file. If I define two parameters sets for the same dihedral, are the
energies added up or is the first one replaced by the second one ?
Unfortunately there is no se
Hi all,
to say the truth I already sent a message regarding this subject some
months ago, but since so much time has passed I thought I'd open a new
thread, also because the situation has quite evolved.
I'm trying to set up a simulation of a small (62 residues) protein in
a mixture of water and DM
Simone Cirri wrote:
Hi all,
to say the truth I already sent a message regarding this subject some
months ago, but since so much time has passed I thought I'd open a new
thread, also because the situation has quite evolved.
I'm trying to set up a simulation of a small (62 residues) protein in
a
Hello Xavier,
thank you very much for the quick reply. As I use it in the topol.top file
everything is fine, so the dihedrals should add up.
Cheers,
Flo
On 16.04.2010, at 15:05, XAvier Periole wrote:
>
> On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote:
>
>> Hello,
>>
>> I have a que
On Apr 16, 2010, at 3:22 PM, Florian Dommert wrote:
Hello Xavier,
thank you very much for the quick reply. As I use it in the
topol.top file everything is fine, so the dihedrals should add up.
yes, I noticed you actually mention it in your email :))
Cheers,
Flo
On 16.04.2010, at 15:05
Hi,
In the dihedraltypes section (or any types section), redefining parameters
for the same atom types generates a warning (saying it will use the last)
and halts grompp, unless you use the -maxwarn option.
For CHARMM there will be an exception to this rule in the next release.
But I guess you d
On 16/04/2010 10:47 AM, Joonho Lee wrote:
Dear all,
I am a little bit confused about electrostatic force calculation
and need some clarification about PME.
I normaly use PME for electrostatic force
and rlist(=rcoulomb) is the parameter for real-space calculation.
As you know, rlist is related
Jennifer Casey wrote:
Hello,
I have been using g_wham, but I have a few questions that I can't find
answers to online. When using WHAM, one does not need the forces
between the pull groups to calculate the PMF, yet g_wham won't run
without it. Is there a reason for this?
Hi Jennifer!
As p
nstlist = 50
; ns algorithm (simple or grid) =
ns_type = grid
Oups, you are dong neighbor searching only every 50fs. Are you sure this
is what you want? If you have a biological system this is probably not
often enough. In biological systems people typically
On 15 Apr 2010, at 18:06, Trang wrote:
My target system is a protein with lipid molecules added randomly
(using GENBOX). Running MD, I expect to
I hope you're using a larger van der Waals distance (0.24nm or so)
when inserting the lipids.
broke down the problem, that is, to run md simulati
kecy...@sina.com wrote:
Hello,I want to use spc216.gro and apply the tip3p.itp parameters, but
it would make a mistake for the pre-processor "grompp" ,it said can't
find HW atomtypes, the force file which I used is "ffG43a1.itp". my
tip3p.itp file is as follows:
HW isn't a valid atom typ
Dear All,
I have run a dynamics of protein ligand complex in lipid bilayer dppc
using desmond software and would like to convert the trajectory files
files into gromacs format, is it possible?? if so, please let me know
your suggestions.
Thanks,
Ram
--
gmx-users mailing listgmx-users@gromac
VMD reads Desmond trajectories and writes GMX format ...
Rests the topology to deal with ...
On Apr 16, 2010, at 4:15 PM, ram bio wrote:
Dear All,
I have run a dynamics of protein ligand complex in lipid bilayer dppc
using desmond software and would like to convert the trajectory files
files
Hi Chris.
Thank you for your answer
I tried the 4.0.4 version but unfortunately, it did better but new
errors appeared anyway
so what I test now is another version of FFTW (fftw-2.1.5.tar.gz)
and the "make" command for gromacs 4.0.7 was a success
so the question is : What will be the differe
Thanks Xavier,
Could you make it more eloborate...
Ram
On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole wrote:
>
> VMD reads Desmond trajectories and writes GMX format ...
> Rests the topology to deal with ...
>
> On Apr 16, 2010, at 4:15 PM, ram bio wrote:
>
>> Dear All,
>>
>> I have run a dyna
Well I guess you want to use gmx analysis tools so you'll have to
build the gmx topology of your system when necessary! Often
only a pdb file or a gro file is sufficient.
On Apr 16, 2010, at 5:24 PM, ram bio wrote:
Thanks Xavier,
Could you make it more eloborate...
Ram
On Fri, Apr 16, 2010
Hello,
I have a protein which has 4 Thr residues on its one side. I want to
calculate the potential energy and Sg of water molecules these Thr
residues are facing (up to 10 angstrom). I have a 10ns trajectory and I
might need only 5ns of it. How should I set my index file and which
tools will help
Dear Sebastien:
Perhaps it's obvious, but can you confirm that you used the compilation
options that I posted? My suggestion was not so much that you should try
to compile 4.0.4 but that you should try the options that I posted. So
if you used your original compilation commands with gromacs ve
In case you use the GIT version of the analysis tools you don't need to
convert the trajectories first.
I've added that the analysis tools can read all vmd supported file formats
if GROMACS finds the vmd libraries.
Roland
On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole wrote:
>
> Well I guess
Hi All!
i have been getting this messsage in my log file.
Started mdrun on node 0 Tue Apr 13 14:28:28 2010
Step Time Lambda
00.00.0
Energies (kJ/mol)
Angle G96AngleProper Dih. Improper Dih. LJ-14
jayant james wrote:
Hi All!
i have been getting this messsage in my log file.
Started mdrun on node 0 Tue Apr 13 14:28:28 2010
Step Time Lambda
00.00.0
Energies (kJ/mol)
Angle G96AngleProper Dih. Improp
Hi. I am modelling a putative interaction between two proteins by doing MD of
the docked complex with GROMACS 4.0. But each time I run the MD simulating 200
ps, the evolves in a different manner, and the average coordinates are
different in a loop believed to help to the interaction. When I plot th
Lucio Ricardo Montero Valenzuela wrote:
Hi. I am modelling a putative interaction between two proteins by doing MD of
the docked complex with GROMACS 4.0. But each time I run the MD simulating 200
ps, the evolves in a different manner, and the average coordinates are
different in a loop believe
Hello, I had posted this message yesterday,maybe it was missing.I want to use
the wall for 2d periodic boundary, but I don't know how to set the wall_type
and wall_density, I don't know what thay depend on for setting. I also want to
know the format of them for setting.
Thank you !--
gmx-u
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