I saw the final .xtc loaded on the first frame .pdb
and got the normal movie.
Sincerely,
Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Tuesday, June 19, 2012 12:38 PM
Subject: Re: [gmx-users] Trjconv error
On 19/06/2012 5:49 PM, Shim
p.
Sincerely,
Shima
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Tuesday, June 19, 2012 11:00 AM
*Subject:* Re: [gmx-users] Trjconv error
On 19/06/2012 4:13 PM, Shima Arasteh wrote:
Dear gmx users,
I want to follow the workflow regarding to
ht
irst frame (
1stframe.pdb ), which I produced earlier?
Thanks for your help.
Sincerely,
Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Tuesday, June 19, 2012 11:00 AM
Subject: Re: [gmx-users] Trjconv error
On 19/06/2012 4:13 PM, Shima Ara
On 19/06/2012 4:13 PM, Shima Arasteh wrote:
Dear gmx users,
I want to follow the workflow regarding to
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for the second step I enter the command as below:
trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb
But I g
Justin mentioned it is due to some
specification in the mpd as for part of your system was selected
only.. Gigi
-E-mail d'origine-
De : Nilesh Dhumal
A : jalem...@vt.edu; Discussion list for GROMACS users
Envoyé le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] t
>>>> Fatal error: Index[2385] 2410 is larger than the number of atoms in
>>>> the trajectory file (2409).
>>>>
>>> This is a consequence of previously outputting some subset of the
>>> atoms above.
>>>
>>
Hello,
I am simulating two carbon nanotubes in water.
1.The two nanotubes are facing each other, end to end, with their end bonded
with polymers.
2. I bonded heavy (molecular weight=10) dummy atoms to the carbon atoms
of the nanotubes, so that they won't move. Each bond length is initially 0,
s
Envoyé le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] trjconv : error
Hello Justin,
As you suggest I used tbpconv
tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o
test.tpr and I selected group 0 for system group (In system group all
atoms are present.)
Still I a
tin
>
>
>>
>> Thanks
>> Nilesh
>>
>>
>>
>>
>> On Wed, May 12, 2010 10:58 am, gigita...@aol.fr wrote:
>>
>>
>>> Hi Nilesh,
>>> If you need the whole system you maybe don't need to include the -n
>>> fl
A : jalem...@vt.edu; Discussion list for GROMACS users
Envoyé le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] trjconv : error
Hello Justin,
As you suggest I used tbpconv
tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr
and I selected group 0 for system group (In system
Justin mentioned it is due to some specification in the mpd as for
> part of your system was selected only.. Gigi
>
>
>
>
>
>
>
>
>
> -E-mail d'origine-
> De : Nilesh Dhumal
> A : jalem...@vt.edu; Discussion list for GROMACS users
>
> E
pd as for part of your system was selected
only..
Gigi
-E-mail d'origine-
De : Nilesh Dhumal
A : jalem...@vt.edu; Discussion list for GROMACS users
Envoyé le : Mercredi, 12 Mai 2010 17:47
Sujet : Re: [gmx-users] trjconv : error
Hello Justin,
As you suggest I used tbpcon
Nilesh Dhumal wrote:
Hello Justin,
As you suggest I used tbpconv
tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr
and I selected group 0 for system group (In system group all atoms are
present.)
Still I am getting the same error.
By selecting "System," you are esse
Hello Justin,
As you suggest I used tbpconv
tpbconv -f 3.trr -s 3.tpr -e 3.edr -n glu-emi-cl-128-no.ndx -o test.tpr
and I selected group 0 for system group (In system group all atoms are
present.)
Still I am getting the same error.
I have one more question,
I am working on solvation glucose i
Nilesh Dhumal wrote:
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
1. trjconv -s 3.tpr -f 3.trr -o b.xtc -center -ur compact -pbc none -n
test.ndx
2. rajconv -s 3.tpr -f b.xtc -o c.xtc - fit rot+trans -n test.ndx
I am getting the following error for step
Hi,
> we have checked it., but of no use it giving some error.,
> for your kind information, this "trjconv_mpi" command works for a protein
> with a drug molecule, a protein moleclue, a dimer, etc..
So it's not trjconv_mpi, it's the trajectory that's wrong.
Could you give the directory listing? (
Hi Parthiban and Sundar,
Did you check the .trr file with gmxcheck?
By the way, is this still that same (faulty) trjconv of these
sysadmins of yours who compiled it with gcc 4.x?
Cheers,
Tsjerk
On Wed, Aug 27, 2008 at 8:36 AM, <[EMAIL PROTECTED]> wrote:
> hi all
>
> i can able to get .trr fi
Wed, 23/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote:
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv error
> To: "Gromacs Users"
> Date: Wednesday, 23 April, 2008, 11:44 AM
> Ragothaman Yennamalli wrote:
> > Hi,
> > Sor
Ragothaman Yennamalli wrote:
Hi,
Sorry for not replying immediately.
Gromacs ver 3.2.1
OS is Red hat enterprise 4
Initially I had tried reading the file from an external hard disk and now I
copied it to another system and tried again. Still the same error.
The reason why I was truncating was du
ark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv error
> To: "Discussion list for GROMACS users"
> Date: Friday, 18 April, 2008, 8:09 PM
> Ragothaman Yennamalli wrote:
> > I wanted to truncate a trajectory file and when I use
> > trjconv tool, I ge
Ragothaman Yennamalli wrote:
I wanted to truncate a trajectory file and when I use
trjconv tool, I get an error:
Fatal error:
/media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc
is not a trj file, exiting
The file is able to read by gmxcheck...
What could be the problem?
What GROMACS versio
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