Thanks Mark. I have several polymer chains (single polymer type) each
having 362 atoms. So in order to exclude all nonbonded interactions of
a chain with itself I need to add about 362 lines in the top file.
[exclusions]
1 2 3 362
2 3 4 362
3 4 5 ...362
.
358 .. 362
.
.
360 361 362 (this i
On 13/04/2012 10:44 AM, Juliette N. wrote:
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at t
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at the end grompp crashes (Killed).
This even lea
Juliette N. wrote:
On 1 April 2012 20:17, Mark Abraham wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
-rerun should break the total nonbo
On 1 April 2012 20:17, Mark Abraham wrote:
> On 2/04/2012 10:10 AM, Juliette N. wrote:
>>
>> Hi all,
>>
>> I have an enquiry regarding calculation of heat of vaporization by
>> estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
>> -rerun should break the total nonbonded e
neighbour searching every configuration.
Mark
Best,
-- Forwarded message --
From: Juliette N.
Date: 1 April 2012 22:10
Subject: Re: [gmx-users] mdrun -rerun
To: Discussion list for GROMACS users
On 1 April 2012 22:07, Mark Abraham wrote:
On 2/04/2012 12:05 PM, Juliett
Hi all,
Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?
Best,
-- Forwarded message --
From: Juliette N.
Date: 1 April 2012 22:10
Subject: Re: [gmx-users] mdrun -rerun
To: Discussion list for GROMACS users
On 1 April 2012 22:07, Mark Abraham wrote
On 1 April 2012 22:07, Mark Abraham wrote:
> On 2/04/2012 12:05 PM, Juliette N. wrote:
>>
>> Thanks. One last question. So whats the new trr file provided by -o
>> flag of mdrun rerun below?
>>
>> mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
>
>
> If it even writes one,
On 2/04/2012 12:05 PM, Juliette N. wrote:
Thanks. One last question. So whats the new trr file provided by -o
flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
If it even writes one, it will be identical to the -rerun file. There's
no way for t
Thanks. One last question. So whats the new trr file provided by -o
flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
>> On 1 April 2012 20:17, Mark Abraham wrote:
>>>
>>> On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I ha
On 2/04/2012 11:16 AM, Juliette N. wrote:
On 1 April 2012 20:17, Mark Abraham wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
-rerun should
On 1 April 2012 20:17, Mark Abraham wrote:
> On 2/04/2012 10:10 AM, Juliette N. wrote:
>>
>> Hi all,
>>
>> I have an enquiry regarding calculation of heat of vaporization by
>> estimating intermolecular nonbonded energies using mdrun rerun option. mdrun
>> -rerun should break the total nonbonded e
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option.
mdrun -rerun should break the total nonbonded energy coming from
nonboded energy of (different molecules
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option.
mdrun -rerun should break the total nonbonded energy coming from nonboded
energy of (different molecules + a molecule with itself). By setting
appropria
On 25/11/2011 2:28 AM, Vasileios Tatsis wrote:
Dear Gromacs Users,
I am using the -rerun option of mdrun to re-analyze a trajectory.
Thus, I tried to rerun the same trajectory (md.xtc) with exactly the
same md.tpr.
But the bonded interactions are not computed or written to the log
file or to
Dear Gromacs Users,
I am using the -rerun option of mdrun to re-analyze a trajectory. Thus, I
tried to rerun the same trajectory (md.xtc) with exactly the same md.tpr.
But the bonded interactions are not computed or written to the log file or to
the .edr file, resulting to completely different
: RE: [gmx-users] mdrun -rerun: bonded interactions of protein
Quoting NG HUI WEN :
> Dear Mark and Justin,
>
>
>
> I have a potentially silly question here. I have been trying to work
out
> the figures from the various options of g_energy. You mentioned before
> that the
by decomposing various potential energy terms. The PME term
cannot be decomposed, for one. Even though you've gotten a value of Coul-recip
for your various calculations, I don't know how valid the results are.
-Justin
>
>
> HW
>
>
>
>
>
> From: gmx-users-boun
n list for GROMACS users
Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein
On 11/11/2010 7:46 PM, NG HUI WEN wrote:
Thanks a lot Justin and Mark for your useful input.
Indeed Justin was right, the quest to dissect the total energy of the
system to get that contribu
PM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] mdrun -rerun: bonded interactions of protein
On 10/11/2010 11:29 PM, NG HUI WEN wrote:
Hi Gmxusers,
I have been trying to run mdrun --rerun to get the energy of the
protein in my protein-lipid system. I know similar questions
trying to make sense of these (and other)
values.
Thanks a bunch again!
HW
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
Sent: Wednesday, November 10, 2010 9:08 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] md
On 10/11/2010 11:29 PM, NG HUI WEN wrote:
Hi Gmxusers,
I have been trying to run mdrun --rerun to get the energy of the
protein in my protein-lipid system. I know similar questions have been
raised on this topic before, I have tried to glean useful information
from them to solve my problem b
NG HUI WEN wrote:
Hi Gmxusers,
I have been trying to run mdrun –rerun to get the energy of the protein
in my protein-lipid system. I know similar questions have been raised on
this topic before, I have tried to glean useful information from them to
solve my problem but unfortunately to n
Hi Gmxusers,
I have been trying to run mdrun -rerun to get the energy of the protein
in my protein-lipid system. I know similar questions have been raised on
this topic before, I have tried to glean useful information from them to
solve my problem but unfortunately to no avail. Thanks for your
I just checked the 3.3.1 source code in md.c and the box is copied
from the xtc file.
I don't know where your problems could come from.
Berk.
From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users
Dear Michel,
Are you sure you're using 3.3.1? I have not checked this specific
issue -- but I have checked that if I run hydration free energy
calculations in patched 3.3.0, and again in patched 3.3.1, and do my
usual free energy analysis using mdrun -rerun, I get the same values.
That either tell
Hi gromacs people,
I was trying to rerun old xtc trajectories to recalculate some energies
involving the solvent, using gmx 3.3.1. I saw important discrepancies
with the original energies (nstlist=1, xtc unaccuracy tolerated). After
some struggling, I figured out that the box size is determine
Hi all.
I think I'm having a really strange problem:
Well, I have some simulations being performed, and wanted to remove from the
bigger molecules any vdw or coulombic intramolecular interaction "longer"
than 1-4. So, from 1-5 included forward, I would like to remove from the
energetic calculatio
Yes of course I looked at the output but I thought is I specify energy
groups it will output only those specified and not the whole system.
However I tried a short run and it did output both. For the crash it
turned out it is because all the nodes try to read the huge trajectory
file at the sam
George Abadir wrote:
Hi all,
I am running simulations of carbon nanotubes and amino acids in
water. I need to calculate the potential energies for the whole system
as well as the interaction energy between the CNT and amino acid. What
I am tried to do is to calculate the energy for th
Hi all,
I am running simulations of carbon nanotubes and amino acids in
water. I need to calculate the potential energies for the whole system
as well as the interaction energy between the CNT and amino acid. What
I am tried to do is to calculate the energy for the whole system first
David,
My conclusion so far is that trr file must be used for
rerun (we learn
every day, isn't it fabulous !)
and I do not see the bug you pointed out but probably
due to the system
I run !!
Well, that sounds like good news.
If we accept to not understand why you got a different
result,
Xavier,
> My conclusion so far is that trr file must be used for rerun (we learn
> every day, isn't it fabulous !)
> and I do not see the bug you pointed out but probably due to the system
> I run !!
Well, that sounds like good news.
I am not surprised that the reduced precision trajectories giv
David,
I'll try to explain a bit better and I attached a gziped pdf file
containing a reduced set of energies
that I sent at my first post.
I, too, am slightly confused about what exactly the differences are
you're seeing. Could you perhaps make a little table or something?
Partly, I just do
Xavier,
I basically rerun a simulation, both in xtc and trrformat,using slightly different tpr file, varying the gro file
used to construct it, and different gmx version, 3.2 and3.3. From those rerun I extracted and compared the bondedand non-bonded energies.The most stricking is that I do not see
Dear Mark,
I basically rerun a simulation, both in xtc and trr
format,
using slightly different tpr file, varying the gro file
used to construct it, and different gmx version, 3.2 and
3.3. From those rerun I extracted and compared the bonded
and non-bonded energies.
The most stricking is that
Xavier Periole wrote:
The energies indicate that:
0) I see a systematic difference with the original energies (not
significant), but using
the trr file helps getting better.
1) I do not see ANY difference between the rerun using the two tpr file
(Unexpected ?!?!)
2) I do not see significant
I forgot the energy file. It is now attached.
XAvier
--
--
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-
Dears,
I have reruning simulations using gmx3.2 and found out some deferences
between the original and rerun energies. I found the posts made by David
Mobley and Mickael Shirts about this issue. Accordingly I downloaded
gmx3.3 and compiled it with the fixed md.c for the rerun, found in the
bugzi
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