hey have a look http://www.com-im6.net/finance/
Kowsar
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Hi,
Welcome! :-) Sincerely,
Shima
From: marzieh dehghan dehghanmarz...@gmail.com
To: gmx-users@gromacs.org
Sent: Thursday, September 20, 2012 10:11 PM
Subject: [gmx-users] hi
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gmx you really should look into this http://www2.worldnews13now.com/1/ see ya
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gmx its about time people saw the value of the internet
http://www.newsl3ireports.com/1/ see ya
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Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is stop
due to any reason?
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On 29 May 2011 14:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is stop
due to any reason?
You can supply the checkpoint file written out, by -cpi option to
thanx sarath 4r reply..can u expalin little bit more..I did not get from
mdrun -h.
On , Sarath Chandra Dantu dsar...@gwdg.de wrote:
On 29 May 2011 14:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run
On 29/05/2011 10:45 PM, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power
problem final md run not completed means initiating md from where is
stop due to any reason?
Please use a meaningful subject line in emails. See
On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote:
Hi all..
I want to ask if it is possible to restart the md run if due to power problem
final md run not completed means initiating md from where is stop due to any
reason?
Suppose your .tpr is topol.tpr
mdrun -cpi state.cpt
Or
Hi,
I am starting with GROMACS. About the units in GROMACS,
I read in the manual that one can use the reduced units
for lennard-jones systems. It means that if I want to use
reduce units I just write the values of all the parameters
(distance, mass, charge ...) in reduced units for all
files
On 2010-08-07 15.22, poj...@icp.uni-stuttgart.de wrote:
Hi,
I am starting with GROMACS. About the units in GROMACS,
I read in the manual that one can use the reduced units
for lennard-jones systems. It means that if I want to use
reduce units I just write the values of all the parameters
I have to recreate .gro file from .trr file by using trjconv which i
have deleated previously for disk space reasons , im using following
commond for that
trjconv -f full.trr -s full.tpr -o fullout.gro .
so my question is will this commond give me the same gro file that it
Please use a descriptive subject line. Simply using Hi will often not attract
the attention of someone who can help you, and other times will get trapped in a
spam filter, depending on the settings of the server or email client.
pavan payghan wrote:
I have to recreate .gro file from
Dear all,
my self ashish and i am trying to dynamics using gromacs.
i am new in these field. in the time of running Pdb2gmx to create .gro
file. i am geting these error.
Fatal error:
Atom HA in residue MET 1 not found in rtp entry with 9 atoms
please help me sortout these problem.
try the option -ignh, it will ignore the the hydrogen atoms in your
pdb file and generate the ones necessary to the force field you choose.
On Dec 15, 2009, at 9:52 AM, ashish pandey wrote:
Dear all,
my self ashish and i am trying to dynamics using gromacs.
i am new in these
Please choose an informative subject line pertinent to the content of your
message; messages that have simply greetings often get blocked by spam filters,
and furthermore do not often rouse the interest of someone who may be able to
help you.
pawan raghav wrote:
Which files should be
Which files should be downloaded to use GRACE and in which directory should
be installed to use xmgrace command.
--
Pawan
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I am new to Gromacs using it with Amber force field amber03,
i am able 2 run my system of DNA till steepest descent but when
i tried to run it for cg it showed
that can not work with so much of constrains so i tried to run
it with -Dposres
Please choose an informative subject line, as it will help attract the attention
of someone interested in helping you.
PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE. wrote:
I am new to Gromacs using it with Amber force field amber03,
i am able 2 run my system
hi,
I am trying to install GROMACS (version 4.0) on my local machine. I tried to
follow the supplied simple instruction in the INSTALL file. The ./configure
step works but the make command doesnt work. My bash prints out make:
*** No targets specified and no makefile found. Stop.
What should i
Amit Choubey wrote:
hi,
I am trying to install GROMACS (version 4.0) on my local machine. I
tried to follow the supplied simple instruction in the INSTALL file. The
./configure step works but the make command doesnt work. My bash
prints out make: *** No targets specified and no makefile
Here I found one amazing website .
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I want to perform simulation of transmembrane
peptide. I have a perseuillibrated POPO (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert .pdb to .gro using
pdb2gmx, it shows the following error
Fatal error:
Residue popc not found in residue
Moutusi Manna wrote:
I want to perform simulation of transmembrane
peptide. I have a perseuillibrated POPO (hydrated)
bilayer (using CHARMM),containing more than 32,000
atom. But when I try to convert .pdb to .gro using
pdb2gmx, it shows the following error
The role of pdb2gmx is not
Dear all gmx-users,
Sorry to bother you.
I am trying to make a molecule with a unit charge well-distributed. But I do
not know how to write such *.top file. Does every atom get the same charge
at the beginning? And can we use Gromacs to simulate the changes of the
charge distribution?
Any help
uki zhu wrote:
Dear all gmx-users,
Sorry to bother you.
I am trying to make a molecule with a unit charge well-distributed. But
I do not know how to write such *.top file. Does every atom get the same
charge at the beginning? And can we use Gromacs to simulate the changes
of the charge
On 8/15/07, Mark Abraham [EMAIL PROTECTED] wrote:
vinod kumar wrote:
Hi, gmx-users,
HI , how to overcome this problem
the output after grompp if em.mdp
fatal error : number of coordinates in coordinate file ( solvated.gro8655)
does not match topology ( top.top 8657
Hi, gmx-users,
HI , how to overcome this problem
the output after grompp if em.mdp
fatal error : number of coordinates in coordinate file ( solvated.gro 8655)
does not match topology ( top.top 8657)
i have made necessary changes in the .top file with respect to the out
put of genbox
vinod kumar wrote:
Hi, gmx-users,
HI , how to overcome this problem
the output after grompp if em.mdp
fatal error : number of coordinates in coordinate file ( solvated.gro 8655)
does not match topology ( top.top 8657)
i have made necessary changes in the .top file with respect
Hi
I am new to Gromacs.
I would like to simulate oligoether branched polysiloxanes in gromacs. I
have the force field availble for the same
Whether gromacs will support force filed for polymers containing hetreo
atmos like silicon?
If so how can I incoroprate this into gromacs?
and also
How to
ann rose wrote:
Hi
I am new to Gromacs.
I would like to simulate oligoether branched polysiloxanes in gromacs. I
have the force field availble for the same
Whether gromacs will support force filed for polymers containing hetreo
atmos like silicon?
Yes - this information is part of the force
for GROMACS users gmx-users@gromacs.orgSubject: [gmx-users] Hi...Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Dear AllHi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field.As you said it depends upon the users taste which
As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature
message:
*From: *Navratna Vajpai [EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]
*Date: *September 13, 2006 10:32:21 AM GMT+02:00
*To: *Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
*Subject: **[gmx-users] Hi...*
*Reply-To: *Discussion list for GROMACS users gmx
Dear Eric.. Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field.As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from
Dear MarkHello.The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN.
Navratna Vajpai wrote:
Dear Prof. David
Thanks for the suggestion. I just had a look for the various force field
options. before starting my simulation I have a little queries..
1) Can I not use the same GROMOS force field g43b1 and then add HA
afterwards by any other software or any other
Dear All .. I have only recently started the GROMACS package. I want to run a MD simulation in vacuum for 5 ns say. I have tried to edit the demo file which comes with the GROMACS package. but Some how it give an error. Which I am still unable to solve. I am atttaching the file under this. Could
Dear All... I was trying to move further and finally managed to move forward. I am explaining the problem in little more detail. The problem arises when the grompp before the mdrun is executed. I don't know why but it ask for -n option for its execution. I tried that also but still the error
Navratna Vajpai wrote:
Dear All ..
I have only recently started the GROMACS package. I want to run a MD
simulation in vacuum for 5 ns say. I have tried to edit the demo file
which comes with the GROMACS package. but Some how it give an error.
Which I am still unable to solve. I am atttaching
Hey Mark..I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the
Navratna Vajpai wrote:
Hey Mark..
I had attached the file along with the mail. I think you could
not receive it. let me paste the contents and explain it little more.
I am trying to run the simulation in vacuum of a nona peptide. I managed
to get pdb2gmx working and even further the EM
On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote:
Navratna Vajpai wrote:
Hey Mark..
I had attached the file along with the mail. I think you could
not receive it. let me paste the contents and explain it little more.
I am trying to run the simulation in vacuum of a nona
Navratna Vajpai wrote:
Dear All
I have been able to carry on with the MD run of my peptides. But when I
converted the traj into the pdb file I realized that there are no HA
atoms in the pdb. I checked the rtp file and found that even those atoms
are not defined there. So can anyone tell me
hi today i have tried to run the position restrained dynamics using my tpr file
grompp -f pr.mdp -c 7/trp_b4pr.gro -p 1/trp.top -o 8/trp_pr.tpr
But its showing the error
Fatal error:
number of coordinates in coordinate file (7/trp_b4pr.gro, 14580)
does not match topology (1/trp.top,
santosh naik wrote:
grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
here the programme was failed showing the error
Fatal error:
No such moleculetype Na
i have checked the ions .itp
its having the information Na atom than why its showing this i could
n't understand
can any one help me
Dear Santosh,
check what forcefield u have used...
whatever forcefield u use, add ions as per its recommended format
specified in ions.itp. Read ions.itp carefully... if it is GROMOS96,
u have to change Na to NA+ and likewise...
all the best...
bharat
On Wed, 5 Apr 2006, santosh naik
Hi all!!!
I am using the programme grompp (double precision) and the programme genion to make neutral .top and .tpr files. But after change the quantity of H2O molecules and add the line with the necessary Na+ ions I am still havingWARNING and the charge is STILL negative. What happend? What am
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