Dear all gmx-users,
I have recently been testing the REMD
simulations. I was running simulations on a supercomputer system based
on the AMD Opteron 12-core (2.1 GHz) processors. The Gromacs 4.5.3
version was used.
I have a system of 5172 atoms, of which 138
atoms belong to solute and the
On 7/02/2011 9:52 PM, Qiong Zhang wrote:
Dear all gmx-users,
I have recently been testing the REMD simulations. I was running
simulations on a supercomputer systembased on the AMD Opteron 12-core
(2.1 GHz) processors. The Gromacs 4.5.3 version was used.
I have a system of 5172 atoms, of whi
Dear User
I am doing MD on protein complex keeping backbone as well as side
chain of all residues which is not on th interface fixed. For this I
prepared posre_backbone_sidechain.itp and defined this in .top file
for full MD. Now I want to know from the trajectory the best side
chain conformation o
shahid nayeem wrote:
Dear User
I am doing MD on protein complex keeping backbone as well as side
chain of all residues which is not on th interface fixed. For this I
prepared posre_backbone_sidechain.itp and defined this in .top file
for full MD. Now I want to know from the trajectory the best
That means in energy group in .mdp file I should write interface.ndx
and tell me if on interface there is hydrogen bond then its value I
will get or not.
Shahid Nayeem
On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear User
>> I am doing MD on protein c
shahid nayeem wrote:
That means in energy group in .mdp file I should write interface.ndx
No, you specify the names of the desired groups using the energygrps keyword,
not the name of the .ndx file. You pass the .ndx file to grompp.
and tell me if on interface there is hydrogen bond then
Dear all,
I'm trying to install gromacs 4.5.3, I've succesfully installed fftw
3.3.2 and openmpi 1.4.3
When I try to configure gromacs with
./configure --with-fft=fftw3 --enable-shared --enable-mpi
the shell reply me with this error:
configure: error: cannot compute sizeof (off_t)
See `conf
Hi Mark,
Many thanks for your fast response!
What's
the network hardware? Can other machine load influence your network
performance?
The supercomputer system is based on the
Cray Gemini interconnect technology. I suppose this is a fast network
hardware...
Are
the systems in the NVT ensembl
Dear users
I tried free energy calculation but grompp couldn't go through. It stops
after
***
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours m
On 8/02/2011 1:48 AM, Qiong Zhang wrote:
Hi Mark,
Many thanks for your fast response!
/What's the network hardware? Can other machine load influence your
network performance?/
The supercomputer system is based on the Cray Gemini interconnect
technology. I suppose this is a fast network har
Hello,
I have an input structure with poor torsion angles and after minimization with
gromacs (both steepest descent and congugate gradient) I found that they were
not corrected. There is enough free space for the torsion angles to be
corrected.
(I am sure of this because when I run the same
hi,
I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about 200. Is it
possible the source code limit the size of the protein that can be
decoupled?
thanks.
dawei
On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li wro
Hi,
As I haven seen in many papers regarding molecular dynamics and in
particular, using the Gromacs software, it seems a common feature to do
a gradually increase of temperature previous to do the final production
run. I noted that some researches do not use simulating annealing
algorithm to do h
Well. It actually isn't dead but becomes very slow for large proteins.
dawei
On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li wrote:
> hi,
>
> I did more test and found that it depended on size of the protein. Grompp
> will die when number of atoms of the protein is larger than about 200. Is it
> pos
Dawei,
I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?
Thank you,
TJ Mustard
On February 7, 2011 at 9:31 AM Da-Wei Li wrote:
Well. It actually isn't dea
Osmany Guirola Cruz wrote:
Hi,
As I haven seen in many papers regarding molecular dynamics and in
particular, using the Gromacs software, it seems a common feature to do
a gradually increase of temperature previous to do the final production
run. I noted that some researches do not use simulat
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This is a
test case only and the protein is 1UBQ. Grompp wills top for about 10
minutes then go through.
***output of grompp*
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
Generated 2278 of
Da-Wei Li wrote:
hello
Here they are the command line and mdp file. I use Gromacs 4.5.3. This
is a test case only and the protein is 1UBQ. Grompp wills top for about
10 minutes then go through.
The efficiency of this kind of process will depend on the amount of available
memory on the s
Da-Wei,
Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?
And are you doing hydration of a protein?
Thank you,
TJ Mustard
On February 7, 2011 at 10:23 AM "Justin A. Lem
hello
My goal is to study the solvation free energy of a fixed protein and compare
it with implicit model. The pr1. mdp is just a test case. Grompp always need
more than 10 minutes to finish for my 76 residues protein when free_energy =
yes, no matter there is PR or not, whether I switch off only
hi, all
I get another strange error. Once I turn on free energy calculation. mdrun
will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13
Minimu
Hi,
I recently converted a PDB file to a .gro using pdb2gmx and I noticed that
the .gro truncates and rounds a digit from the atomic co-ordinates. Am I
making a mistake somewhere?
For example on atom 1, the .pdb file lists the co-ordinates:
-> 35.375 22.352 -11.970
where the .gro lists:
-> 3.538
I have the following doubts about position restrain mdp file:
Position restraint should be done with pressure coupling?
Would you recommend a number of nsteps when doing position restraint,
for example for a protein having 600 aminoacids?
Thanking in advance,
Osmany
--
gmx-users mailing li
Matthew Chan wrote:
Hi,
I recently converted a PDB file to a .gro using pdb2gmx and I noticed
that the .gro truncates and rounds a digit from the atomic co-ordinates.
Am I making a mistake somewhere?
For example on atom 1, the .pdb file lists the co-ordinates:
-> 35.375 22.352 -11.970
whe
Osmany Guirola Cruz wrote:
I have the following doubts about position restrain mdp file:
Position restraint should be done with pressure coupling?
Equilibration (with or without restraints) should be done under the conditions
you wish to model.
Would you recommend a number of nsteps wh
Da-Wei,
How do you generate your box, solvent, ions?
I use this sequence of commands:
pdb2gmx -f protein.pdb -o protein.gro -p protein.top
editconf -bt cubic -f protein.gro -o protein.gro -c -d 1.5
genbox -cp protein.gro -cs spc216.gro -o protein_b4
Da-Wei Li wrote:
hi, all
I get another strange error. Once I turn on free energy calculation.
mdrun will complain this:
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
multi-body bonded interactions: 0.428 nm, Proper
On 8/02/2011 2:47 AM, abdullah ahmed wrote:
Hello,
I have an input structure with poor torsion angles and after
minimization with gromacs (both steepest descent and congugate
gradient) I found that they were not corrected. There is enough free
space for the torsion angles to be corrected.
(I
On 8/02/2011 12:58 AM, vferra...@units.it wrote:
Dear all,
I'm trying to install gromacs 4.5.3, I've succesfully installed fftw
3.3.2 and openmpi 1.4.3
When I try to configure gromacs with
./configure --with-fft=fftw3 --enable-shared --enable-mpi
the shell reply me with this error:
configur
hello
1. I used almost identical comands with you.
2. If I set "couple-intramol = yes". My grompp will run very fast.
>From the manu, "couple-intramol = no means " all intramol (protein-protein
interaction in my case) interaction are turned to predefind list while
"couple-intramol
Da-Wei Li wrote:
hello
1. I used almost identical comands with you.
2. If I set "couple-intramol = yes". My grompp will run very fast.
From the manu, "couple-intramol = no means " all intramol
(protein-protein interaction in my case) interaction are turned to
predefind list w
Hi all,
I have been having issues with my system blowing up due to bad contacts. All of these contacts have been made by me when I have tried to "dock" or align my protein with my ligand in pymol. I do what I can to limit while still having the correct geometry and also being
TJ Mustard wrote:
Hi all,
I have been having issues with my system blowing up due to bad contacts.
All of these contacts have been made by me when I have tried to "dock"
or align my protein with my ligand in pymol. I do what I can to limit
while still having the correct geometry and also
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