On 30/04/2011 11:37 PM, Faezeh Kargar wrote:
> On 4/30/2011 7:22 PM, Faezeh Kargar wrote:
>>
>> Dear gmx users,
>>
>> My code stops running because of electricity voltage oscillation. it
>> happened for several times and each time I restarted running my code.
>> but for this time with command
>
On 1/05/2011 6:56 AM, delara aghaie wrote:
Dear Justin
I have started lyzosyme tutorial. when using the command pdb2gmx I
get the following error.
Please guide me to solve it
thanks
Regards
D. Aghaie
Program pdb2gmx, VERSION 4.0.99-dev-20100315
Source code file:
/apps/gromacs/build/gromac
Dear gromacs users,
I am a new user of gromacs. I am currently trying to build a large
bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and
no protein embedded in it. I have used single lipids from
pre-equilibrated bilayers available at Mr. Tieleman's website. The
distan
Dear Justin
I have started lyzosyme tutorial. when using the command pdb2gmx I get the
following error.
Please guide me to solve it
thanks
Regards
D. Aghaie
Program pdb2gmx, VERSION 4.0.99-dev-20100315
Source code file: /apps/gromacs/build/gromacs-4.5-beta3/src/kernel/pdb2top.c,
line: 147
If you are sure about the force field (the one from Lopes et al.?) you
are using, build a dilute system, and then run long enough simulations
using NTP ensemble. possibly using simulation annealing.
? 2011-4-30 16:44, Vitaly Chaban ??:
I am trying to create an ionic-liquid system
Maria Hamilton wrote:
Hi all
I need .itp and .mdp files of some Alkanes such as Hepane, Decane and
Heptene, Decene in Amber forcefield.
Would you please help me?
Such species should be trivial to generate using antechamber (with GAFF,
perhaps). There are various scripts to convert fro
>
>
> I am trying to create an ionic-liquid system comprising of
> 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have
> generated the system using following command:
> genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb
> , well it created syst
> On
4/30/2011 7:22 PM, Faezeh Kargar wrote:
>>
>> Dear
gmx users,
>>
>> My code stops running because of
electricity voltage oscillation. it
>> happened for several
times and each time I restarted running my code.
>> but for
this time with command
>>
>> mdrun -s topol.tpr
-x
>> traj.part0002
Hi all
I need .itp and .mdp files of some Alkanes such as Hepane, Decane and
Heptene, Decene in Amber forcefield.
Would you please help me?
Best Regards
Thanks alot
Maria
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On 2011-04-30 14.17, Zoe Hall wrote:
Gmx-users,
I am trying to carry out a simulation of lysozyme in vacuo using the
OPLS-AA forcefield. After energy minimisation, the protein is run for
10ps with position restraints and temperature coupling on. This is
followed by the full production run of 10n
Gmx-users,
I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA
forcefield. After energy minimisation, the protein is run for 10ps with
position restraints and temperature coupling on. This is followed by the full
production run of 10ns with temperature and pressure c
On 4/30/2011 7:22 PM, Faezeh Kargar wrote:
Dear gmx users,
My code stops running because of electricity voltage oscillation. it
happened for several times and each time I restarted running my code.
but for this time with command
mdrun -s topol.tpr -x
traj.part0002.part0003.part0004.part00
On 2011-04-30 00.38, Mark Abraham wrote:
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
×M5~˪yïxã]¹ß]7ãMuÓ
Program mdrun, VERSION 4.0.7Source
code file: checkpoint.c, line: 565Fatal error:Attempting
to read a checkpoint file of version 12 with code of version 4-- 83_kargar--
This message has been scanned for viruses and
dangerous content by
MailScanner, and is
believed to be clea
On 4/30/2011 4:47 AM, Charlie Forde wrote:
Thank you Mark for your response,
In carrying out the test you recommended I realised that I had set the
integrator to sd, in such a case the tcoupl parameter is ignored. This
explains my well behave temperature in the absence of setting a tcoupl
opt
On 4/30/2011 9:06 AM, Juliette N. wrote:
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few
steps I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560,
On 4/30/2011 8:50 AM, Juliette N. wrote:
Dear experts,
I have successfully installed a normal gromacs 4.5.4 installation on
one of my machines.
I have read the Installation Instructions that "As of GROMACS 4.5,
threading is supported, so for e.g multi-core workstations, MPI is no
longer req
On 4/30/2011 3:54 PM, saly jackson wrote:
Hi all
I want to know about the ability of GROMACS to simulate sulfate in(SO4
(2-)),
Do we can have the ion in our simulation using GROMACS?
You asked this question on Wednesday, and got an answer. Googling
"sulfate gromacs" finds that answer. If you
On 4/30/2011 5:20 PM, Prema Awati wrote:
*/-- Original Message --/*
From: prem...@iiserpune.ac.in
To: gmx-users@gromacs.org
Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30)
Subject: ionic liquids
Sir,
I am trying to create an ionic-liquid system comprising of
1-butyl-3-methyl-imidazolium(bmi
-- Original Message --
From: prem...@iiserpune.ac.in
To: gmx-users@gromacs.org
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