On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury wrote:
> You need to re submit the jobs, with decreased time.
>
And next time check with the manual and consider your needs before making
arbitrary choices :-)
Mark
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Apr 6, 20
Dear Mark and Chandan kumar Choudhury
Thank you very much from your answers. May I know what is the best of frequency
to write the output (In MARTINI), Please?
Best Regards
Dina
On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury wrote:
You need to re subm
On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy wrote:
> There was no fatal error preceding the output. After selecting the groups
> following are the output on the screen
> Reading frame 1 time0.100
> Warning: can not make broken molecules whole without a run input file,
> don't
Only you can judge that, because only you know what you are trying to
observe.
Mark
On Sat, Apr 6, 2013 at 10:54 AM, dina dusti wrote:
>
>
>
>
>
>
> Dear Mark and Chandan kumar Choudhury
> Thank you very much from your answers. May I know what is the best of
> f
How about reading the literature on combining AMBER and Berger? :-)
Mark
On Sat, Apr 6, 2013 at 8:24 AM, James Starlight wrote:
> Dear Gromacs Users!
>
>
> I'm looking for cut-offs parameters which would be suitable for the
> simulation of the membrane proteins (bergers united-atom lipids) with
On Sat, Apr 6, 2013 at 5:56 AM, Juliette N. wrote:
> Thank you Justin. I have now the topology. I have a quick question
> regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
> respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
> these are not the pro
Thanks from your help.
Best Regards
Dina
From: Mark Abraham
To: dina dusti ; Discussion list for GROMACS users
Sent: Saturday, April 6, 2013 1:27 PM
Subject: Re: [gmx-users] nstxout, nstvout, . . .
Only you can judge that, because only you know what you
Hello:
I saw lots of people is using gromos54a7_lipid FF and I search the
gromacs webiste, but didn't find it. Would anybody tell me where can we
obtain it?
THX
Albert
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Respected Sir,
Now I am trying an REMD simulation on a peptide in
cluster. The command line I used as follows
mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2
-replex 1000 -reseed 175320
But this command line getting error like this
Wrote pdb files
That paper suggests of using 1.0 nm for all cut-offs
http://pubs.acs.org/doi/abs/10.1021/ct200491c
that seems strange to me because with gromos-56 I've used 1.2 nm cutoffs.
James
2013/4/6 Mark Abraham
> How about reading the literature on combining AMBER and Berger? :-)
>
> Mark
>
> On Sat, Ap
Hi all!
I have a problem. So as it can be seen in the theme I am trying to improve
sampling of free energy calculating simulation by using replica exchange.
In the gmx4.6 it is simple while using FEP technique, but does not
implemented for umbrella sampling. But I want evaluate potential of mean
f
It's available in Gromacs format from the Automatic Topology Builder
website:
http://compbio.biosci.uq.edu.au/atb/index.py?tab=forceField_tab
On Sat, Apr 6, 2013 at 6:38 AM, Albert wrote:
> Hello:
>
> I saw lots of people is using gromos54a7_lipid FF and I search the
> gromacs webiste, but di
On Sat, Apr 6, 2013 at 7:17 AM, Shine A wrote:
> Respected Sir,
>
> Now I am trying an REMD simulation on a peptide in
> cluster. The command line I used as follows
>
> mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2
> -replex 1000 -reseed 175320
>
>
On Sat, Apr 6, 2013 at 8:45 AM, James Starlight wrote:
> That paper suggests of using 1.0 nm for all cut-offs
> http://pubs.acs.org/doi/abs/10.1021/ct200491c
>
> that seems strange to me because with gromos-56 I've used 1.2 nm cutoffs.
>
>
And what was your basis for that decision? What makes you
Dear GMX users,
There is a copper ion with four ligands in my system. I am going to
study this system using MD simulations.
For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
one paper will be used in our
simulations. I already found the parameters of copper ion (Cu2+) in t
On 04/06/2013 04:29 PM, Justin Lemkul wrote:
And what was your basis for that decision? What makes you think that
AMBER99 can even be combined with the Berger lipid force field?
-Justin
I think he probably read this paper which suggest the combination of
Amber FF and Berger lipids FF:
htt
On Sat, Apr 6, 2013 at 10:46 AM, Albert wrote:
> On 04/06/2013 04:29 PM, Justin Lemkul wrote:
>
>> And what was your basis for that decision? What makes you think that
>> AMBER99 can even be combined with the Berger lipid force field?
>>
>> -Justin
>>
>
>
> I think he probably read this paper wh
In systems of such kind, everything will depend on the atom of the ligand,
which coordinated by copper ion.
Perform ab initio geometry optimization and find the optimal distance. Then
adjust sigma(s).
Dr. Vitaly Chaban
There is a copper ion with four ligands in my system. I am going to
> s
Hi, i'm new to grimaces and want to run a minimization process in parts, but
i'm having problems extracting the last frame, when i try the following command:
trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e 0
it returns no data, if i try 11 in the frame number it prints out a mode
On Sat, Apr 6, 2013 at 2:23 PM, Juan Antonio Raygoza Garay wrote:
> Hi, i'm new to grimaces and want to run a minimization process in parts,
> but i'm having problems extracting the last frame, when i try the following
> command:
>
> trjconv -s em-vac${ID}.tpr -f em-vac${ID}.trr -o mintmp.pdb -e
Dear:
I am trying to pull my ligand outside of the binding pocket with
following configurations:
title = Umbrella pulling simulation
define = -DPOSRES
; Pull code
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= Y N N
pull_start
On Sat, Apr 6, 2013 at 2:47 PM, Albert wrote:
> Dear:
>
> I am trying to pull my ligand outside of the binding pocket with
> following configurations:
>
> title = Umbrella pulling simulation
> define = -DPOSRES
> ; Pull code
> pull= umbrella
> pull_geometry = distance ;
Dear all,
I need to add 100 molecules of a second solvent to my polymer. I do this in
two solvation steps as below:
genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500
genbox -cp solute-solvent1.gro -ci Solvent2.gro -o solute-solvent1-solvent2.gro
-nmol 100
1- Is this the co
On Sat, Apr 6, 2013 at 5:37 PM, Juliette N. wrote:
> Dear all,
>
> I need to add 100 molecules of a second solvent to my polymer. I do this in
> two solvation steps as below:
>
> genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500
>
> genbox -cp solute-solvent1.gro -ci Solvent
Hi!
I have 6 nodes. Each node has two CPUs,12 cores totally.
How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
performance?
Thanks!
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On Sat, Apr 6, 2013 at 9:11 PM, 陈照云 wrote:
> Hi!
> I have 6 nodes. Each node has two CPUs,12 cores totally.
> How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
> performance?
>
Those options will have a significantly smaller impact on performance than
other factors l
Hi all,
I have a system of peptide/POPC/water/ions. The energy minimization and NVT
steps has passed successfully. I ran NPT step for around 10 ns with restraints
of protein and P atoms at first nano seconds and then removing them gradually.
I tried to go on MDRUN. I did not remove restraint o
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