hey have a look http://www.com-im6.net/finance/
Kowsar
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Hi,
Welcome! :-) Sincerely,
Shima
From: marzieh dehghan
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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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
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
http://www.g
thanx sarath 4r reply..can u expalin little bit more..I did not get from
mdrun -h.
On , Sarath Chandra Dantu 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 not completed m
On 29 May 2011 14:45, 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 mdrun and
continue
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 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
(distan
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 (.mdp
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 .t
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 wa
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 field.
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.
-
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 downloa
Which files should be downloaded to use GRACE and in which directory should
be installed to use xmgrace command.
--
Pawan
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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
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
dire
Hi,
I would like to simulate hard sphere with different charge values (e.g. +30)
and with different diameters (e.g. 5 nm). In addiction, in these models of the
hard sphere I would like to insert dipole (e.g. 15 Debye). So, is this possible
to simulate these models in GROMACS?
Thanks,
Pos-doc.
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
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
Here I found one amazing website .
TryLogIn.com Hey Who knows if the luck is with you. Grab a gift for mere logging in. Just a matter of few minutes to log in each day. A logging in can make you a winner means, is it a big deal? Nothing to loose. Register yourself and come back each day to see you
Here I found one amazing website .
TryLogIn.com Hey Who knows if the luck is with you. Grab a gift for mere logging in. Just a matter of few minutes to log in each day. A logging in can make you a winner means, is it a big deal? Nothing to loose. Register yourself and come back each day to see you
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
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 resi
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 distrib
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 woul
Nice to meet you.
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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 ( s
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, 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
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
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 ge
TECTED]
> >>>> <mailto:[EMAIL PROTECTED]>>
> >>>> *Date: *September 13, 2006 10:32:21 AM GMT+02:00
> >>>> *To: *Discussion list for GROMACS users >>>> <mailto:gmx-users@gromacs.org>>
> >>>> *Subject: **[
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 <mailto:gmx-users@gromacs.org>>
*Subject: **[gmx-users] Hi...*
*Reply-To: *Discussion list for GROMACS us
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 whi
> Nav
> >
> > Begin forwarded 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 >
You are right .. I have used g_rama for the phi-psi values. I will try g_angle as well. With -ve i meant negative values for the phi angle. As far as I understand negative phi values are sterically not allowed. let me check with the g_angle as well. Thanks for the answer as well the reference. bes
Navratna Vajpai wrote:
Sorry for not so explicitly explaining the things.. Here it goes
I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field.
when I used the OPLS-AA the phi angles came out to be -ve for three of
the amino acids. which is stericaly not allowed. But when I ran
Mu Yuguang (Dr) wrote:
OPLS-aa force field is good for beta structure, it is not so good for
alpha helix study.
Amber99f force field is good for alpha helix , but not good for beta
structure
Very encouraging...
--
David.
___
GROMACS users
Subject: Re: [gmx-users] Hi...
Sorry for not so explicitly explaining the things.. Here it
goes
I have a nona peptide and I ran a MD of 20ns using OPLS-AA force
field.
when I used the OPLS-AA the phi angles came out to be -ve for three of
the amino acids. which is stericaly
would be nice. Best regardsNavBegin forwarded 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 mailto:gmx-users@gromacs.org>>*Subject: **[gmx-users] Hi...**Reply-To
;>
*Date: *September 13, 2006 10:32:21 AM GMT+02:00
*To: *Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
*Subject: **[gmx-users] Hi...*
*Reply-To: *Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
Dear All
Hi..
This is in regard to your pre
st for GROMACS users <gmx-users@gromacs.org>Subject: [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 up
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 my
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 prog
Dear Prof. DavidThanks 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 program in your package?2)Can I u
Navratna Vajpai wrote:
Dear Mark
Hello.
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
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. Now
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 how
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 how to get the HA (after or bef
Many thanks Eric, it worked. I didn't really had look into this.Best regardsNavOn Aug 16, 2006, at 11:34 AM, Erik Marklund wrote: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
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 n
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 working
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:
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 t
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 stays.
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 an
> 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 topo
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,
Hi
I had the same problem i needed NA in the .gro (get this by in genion
having -pname NA)
hope this help
Tom
--On Wednesday, April 05, 2006 15:38:22 +0200 Tsjerk Wassenaar
<[EMAIL PROTECTED]> wrote:
Hi :)
Not the box, you probably need NA or NA+. It's case sensitive and depends
on the
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 wrote:
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
Hi :)Not the box, you probably need NA or NA+. It's case sensitive and depends on the force field definition you use. Cheers,TsjerkOn 4/5/06,
Adriana Pietropaolo <[EMAIL PROTECTED]> wrote:
Probably you generated a bad box.Check the box with i.e. rasmol and try to use -princ option in editconf(to
Probably you generated a bad box.
Check the box with i.e. rasmol and try to use -princ option in editconf
(to put the protein in its inertial axes) and genion to make the ions to
ensure charge neutrality.
good luck,
Adriana
> hi
> today i have tried with some other protein but the problem still
hi
today i have tried with some other protein but the problem still persists .
today i will tell you problem in detail
today i have taken the protein pdb file which conatains only the amino
acids no hetero atoms
i have run the pdb2gmx command
pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1
Hello friends again i have faced the problem
this time i have taken the Hydrolase ( TRYPSIN BEFORE A HIGH DOSE
X-RAY "BURN") .i have taken the pdb file.
i have edited the pdb file in the text editor
i have removed all the hetero atoms and
and put them in the dundee prodrg server and collected the
Hi Santosh,
For one thing, you don't want to use the gmx force field. For the rest,
you can safely listen to Lars ;) But it is in general good to read a
bit on the background of the force fields and to read papers regarding
the types of systems you are trying to simulate. From these you can aso
ge
hi santosh,
which force field to use usually dependes on your system. E.g., for DNA,
the AMBER force field is often used. For proteins, you might want to use
GROMOS96 or OPLS, which are quite popular these days. However, this does
not necessarily mean that the other force fields, such as GROMAC
hi friends
i m santosh naik.friends i m new to this field so i m facing a lot of problems dealing with this program.so i wants to start up with simple simulations like proteins in water. my problem is which force field i should use in
pdb2gmx is it default one or some other please can any one w
Marcelo Fabricio Masman wrote:
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 having WARNING and the charge is S
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 having WARNING and the charge is STILL negative. What happend? What a
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