Okay thanks. I got it. :-)
Best Regards,
Jesmin
On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham wrote:
> On 18/08/12, *jesmin jahan * wrote:
>>
>> Hi Mark,
>>
>> Thanks for your reply.
>>
>> In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
>> So, the the LJ energy is coming as
On 18/08/12, *jesmin jahan * wrote:
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So, the the LJ energy is coming as zero. But the coulomb potential is
non zero. What should I do to make it zero?
Each charge-charge interaction contribute
On 8/17/12 6:44 PM, Acoot Brett wrote:
This explaination of Justin is correct. For VMD read trr file, it cannot read
more than 522 frames, and it can read far more than 522 frames of xtc file.
However if the XTC is too large, VMD will gives the error of runtime error. Can
anyone solve this p
This explaination of Justin is correct. For VMD read trr file, it cannot read
more than 522 frames, and it can read far more than 522 frames of xtc file.
However if the XTC is too large, VMD will gives the error of runtime error. Can
anyone solve this problem?
I will try gmxcheck.
Cheers,
On 8/17/12 5:52 PM, Acoot Brett wrote:
Dear Justin,
But it is very difficult to explain why the xtc file gives more frames in VMD
than trr file. Can you explain it? Or VMD has made the modification when read
the xtc file or the trr file?
It is possible that VMD ran out of memory attemptin
Dear Justin,
But it is very difficult to explain why the xtc file gives more frames in VMD
than trr file. Can you explain it? Or VMD has made the modification when read
the xtc file or the trr file?
Cheers,
Acoot
- Forwarded Message -
From: Justin Lemkul
To: Acoot Brett ; Discuss
On 8/17/12 4:33 PM, Acoot Brett wrote:
Dear All,
Follwong is the MD mdp file I used for my production MD, which I downloaded
from
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp.
Clearly it writes how it extract xtp file. Will you please explain t
Dear All,
Follwong is the MD mdp file I used for my production MD, which I downloaded
from
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp.
Clearly it writes how it extract xtp file. Will you please explain to me which
is the command for the extracti
:-)
Thanks Justin.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, August 17, 2012 10:07 PM
Subject: Re: [gmx-users] 4 question
On 8/17/12 1:33 PM, Shima Arasteh wrote:
> Hi,
>
> The .pdb file
On 8/17/12 1:33 PM, Shima Arasteh wrote:
Hi,
The .pdb file either should be dowloaded from RCSB website or you need to
construct the structure by a software such as hyperchem and save the structure
in .pdb format, so you are not supposed to get .pdb output through pdb2gmx
command.
The ou
Hi,
The .pdb file either should be dowloaded from RCSB website or you need to
construct the structure by a software such as hyperchem and save the structure
in .pdb format, so you are not supposed to get .pdb output through pdb2gmx
command.
About the second problem, I think you need to chose t
On 8/17/12 1:19 PM, Hossein Lanjanian wrote:
Hi
we are new academic users of GROMACS. we installed gromacs 4.5.5 and
tried to learn the job by using tutorials found in the "gromacs.org"
web site. There is one question:
we successfully ran the "1PGB.pdb".
we know that *.pdb or *.gro files ar
Hi
we are new academic users of GROMACS. we installed gromacs 4.5.5 and
tried to learn the job by using tutorials found in the "gromacs.org"
web site. There is one question:
we successfully ran the "1PGB.pdb".
we know that *.pdb or *.gro files are necessary for the rest of
analysis however we h
Thank you dear Justin!
Dariush
On Fri, Aug 17, 2012 at 11:04 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5000298...@n6.nabble.com> wrote:
>
>
> On 8/17/12 10:41 AM, dariush wrote:
> > genconf -renumber works well for renumbering. However, after
> minimization
> > of that renumbered .gro fil
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So, the the LJ energy is coming as zero. But the coulomb potential is
non zero. What should I do to make it zero?
Energies (kJ/mol)
GB PolarizationLJ (SR) Coulomb (SR) Potential
On 8/17/12 10:41 AM, dariush wrote:
genconf -renumber works well for renumbering. However, after minimization
of that renumbered .gro file, I have previous numbering.
You always will. The numbering is read from the topology, so simulation output
will always be numbered that way and you wil
genconf -renumber works well for renumbering. However, after minimization
of that renumbered .gro file, I have previous numbering.
Dariush
On Thu, Aug 16, 2012 at 5:54 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5000267...@n6.nabble.com> wrote:
>
>
> On 8/16/12 5:22 PM, dariush wrote:
> > De
On 17/08/2012 6:46 PM, Acoot Brett wrote:
Dear All,
After a production MD, both the xtc file and trr file are produced. trr file is
much larger than the xtc file. But when we openned the original gro file one of
the file from xtc file and trr file in VMD, we will find the xtc contains more
fr
On 8/17/12 5:25 AM, Albert wrote:
Dear:
I am going to check the total charge of my system from a gro file. I am
wondering which command should I use? I check the manual and found nothing for
it.
Charge information is stored in the topology, not the coordinate file.
-Justin
--
On Fri, Aug 17, 2012 at 2:16 PM, Acoot Brett wrote:
>
> Dear All,
>
> After a production MD, both the xtc file and trr file are produced. trr
> file is much larger than the xtc file. But when we openned the original gro
> file one of the file from xtc file and trr file in VMD, we will find the xtc
Dear:
I am going to check the total charge of my system from a gro file. I
am wondering which command should I use? I check the manual and found
nothing for it.
thank you very much
best
A
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Dear All,
After a production MD, both the xtc file and trr file are produced. trr file is
much larger than the xtc file. But when we openned the original gro file one of
the file from xtc file and trr file in VMD, we will find the xtc contains more
frames in comparison with the trr file.
Will
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