Re: [gmx-users] Turn-off the long range Van der Waals interactions

[Krishna Mohan Gupta]

Hi Mark,

Actually, I want to exclude long range interaction potentials (both coulombic 
and LJ) of some of the molecules.


Thanks
Krishna

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Wednesday, March 30, 2016 12:36 PM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Turn-off the long range Van der Waals interactions

Hi,

What do you mean by "long-range Van der Waals interactions?"

Mark

On Wed, Mar 30, 2016 at 4:07 AM Krishna Mohan Gupta 
wrote:

> Dear Gromacs users,
>
> May I know, how to turn-off the long range Van der Waals interactions
> during simulations ?
>
> Thanks
> Krishna
>
>
>
>
>
>
> 
>
> Important: This email is confidential and may be privileged. If you
> are not the intended recipient, please delete it and notify us
> immediately; you should not copy or use it for any purpose, nor
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Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

[sun]

I have not looked at your link yet but I believe PyMol is best for generating 
high quality figures. You can explore a number of options in pymol. 
Regards
Suniba

Sent from my iPhone

> On 30-Mar-2016, at 3:15 am, bio hpc  wrote:
> 
> Hi,
> 
> after a protein-ligand simulation with gromacs, I would like to be able to 
> generate a diagram/figure with information about protein-ligand interactions, 
> something like this:
> 
> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg 
> 
> 
> I had a look to all gromacs tools but found nothing similar to this. Where 
> can I start from?
> 
> Thanks,
> 
> biohpc
> 
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Re: [gmx-users] Turn-off the long range Van der Waals interactions

[Mark Abraham]

Hi,

What do you mean by "long-range Van der Waals interactions?"

Mark

On Wed, Mar 30, 2016 at 4:07 AM Krishna Mohan Gupta 
wrote:

> Dear Gromacs users,
>
> May I know, how to turn-off the long range Van der Waals interactions
> during simulations ?
>
> Thanks
> Krishna
>
>
>
>
>
>
> 
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
> --
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Re: [gmx-users] on the gromacs force field for keep helix

[Tsjerk Wassenaar]

Hi Brett,

There is no GROMACS force field. Now the original GROMOS force fields 53a5
and 53a6 are known to be more unstable in the helix department than they
should, so better not use those. There are newer versions of 53a6 and
there's 54a7, which are fine. I'm actually not entirely sure what version
of the 53a6 version is now included in the GROMACS distribution.

As a side note, don't pin yourself on keeping the helix. If it doesn't want
to keep with nowadays force fields, there's quite a chance that it's not
going to be a helix all the time.

Hope it helps,

Tsjerk
On Mar 30, 2016 04:18, "Brett"  wrote:

> Dear All,
>
> Before I read some on-line material , perhaps the on-line tutorial of
> Justin. It said there was a gromacs force field better than the other
> gromacs force field for keeping the intact of the helix during MD. WIll you
> please tell me which is the force field used for keeping the intact of the
> helix?
>
> Brett
>
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[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

[Christopher Neale]

Dear Users: 

I am trying to do some Hamiltonian replica exchange (H-REMD) in gromacs 5.1.2 
and am running up against really large slowdowns when decoupling a large number 
of atoms. I am decoupling 5360 atoms out of the 15520 atoms in my system. The 
goal is not to get a PMF, but to enhance sampling using the REST approach to 
partially decouple lipids in a bilayer. This approach enhances lipid relaxation 
times ( http://pubs.acs.org/doi/pdf/10.1021/ct500305u ) though the authors of 
that paper modified the gromacs code to do their own H-REMD in order to avoid 
the really slow speed they also got when decoupling lots of atoms via the free 
energy code. 

I have already posted details here http://redmine.gromacs.org/issues/742 , 
which includes .mdp options and some timing output. I compare the timing output 
to a standard temperature REMD (T-REMD) run. For my usage, the slowdown is 
about 12x for H-REMD vs. T-REMD. 

I am motivated to find a solution within gromacs because the alternative is to 
use gromacs 4.6.7 with plumed (or with the aforementioned modified code, which 
is also gromacs v4). Normally that would be a viable option, but I am using the 
charmm force field and the charmm TIP3P water and I would rather not give up 
the speed boost that I see in gromacs v5.1.2, which allows the use of the 
verlet cutoff scheme and has been tested and shown to give the correct 
reproduction of charmm forces (vs. the forces one would get using the charmm 
simulation software).

I took a look at gmxlib/nonbonded/nb_free_energy.c in v.5.1.2, but I was unable 
to find a function called "gmx_waste_time_here()" and beyond that I was out of 
my depth.

Thank you for any pointers,
Chris.


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[gmx-users] on the gromacs force field for keep helix

[Brett]

Dear All,

Before I read some on-line material , perhaps the on-line tutorial of Justin. 
It said there was a gromacs force field better than the other gromacs force 
field for keeping the intact of the helix during MD. WIll you please tell me 
which is the force field used for keeping the intact of the helix?

Brett

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[gmx-users] Turn-off the long range Van der Waals interactions

[Krishna Mohan Gupta]

Dear Gromacs users,

May I know, how to turn-off the long range Van der Waals interactions during 
simulations ?

Thanks
Krishna








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[gmx-users] Turn-off the long range Van der Waals interactions

[Krishna Mohan Gupta]

Dear Gromacs users,

May I know, how to turn-off the long range Van der Waals interactions during 
simulations ?

Thanks
Krishna





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Re: [gmx-users] cgenff CTAB

[Justin Lemkul]

On 3/29/16 6:32 PM, xy21hb wrote:


https://www.dropbox.com/s/bptog3lgtyp9qt2/CTAB.zip?dl=0

Dear Justin,


Above is the link to the mol2 and str files.
I checked the naming of the input files and the same error remained.



It's exactly as I expected; in the stream file you have:

RESI /scrat

and the .mol2 file has a residue named "MOL1" so it doesn't match.

-Justin



Thanks,


Yao





At 2016-03-30 05:42:25, "Justin Lemkul"  wrote:



On 3/29/16 5:40 PM, xy21hb wrote:

Dear all,
I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 
force field in GROMACS.
However, it always gives the wrong error message, saying that the number of 
atoms does not match the .top.
I wonder what could be the reason for this problem.


Usually this means your residue name is specified incorrectly.  Check that your
command line, .mol2, and RESI specification match.


Attached are .mol2 and .str files.


The list does not accept attachments.  If you need to share files, upload them
somewhere and provide a URL.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] cgenff CTAB

[xy21hb]

https://www.dropbox.com/s/bptog3lgtyp9qt2/CTAB.zip?dl=0 

Dear Justin,


Above is the link to the mol2 and str files.
I checked the naming of the input files and the same error remained.


Thanks,


Yao





At 2016-03-30 05:42:25, "Justin Lemkul"  wrote:
>
>
>On 3/29/16 5:40 PM, xy21hb wrote:
>> Dear all,
>> I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 
>> force field in GROMACS.
>> However, it always gives the wrong error message, saying that the number of 
>> atoms does not match the .top.
>> I wonder what could be the reason for this problem.
>
>Usually this means your residue name is specified incorrectly.  Check that 
>your 
>command line, .mol2, and RESI specification match.
>
>> Attached are .mol2 and .str files.
>
>The list does not accept attachments.  If you need to share files, upload them 
>somewhere and provide a URL.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
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[gmx-users] Generate diagram/figure with information about protein-ligand interactions

[bio hpc]

Hi,

after a protein-ligand simulation with gromacs, I would like to be able to 
generate a diagram/figure with information about protein-ligand interactions, 
something like this:

https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg 


I had a look to all gromacs tools but found nothing similar to this. Where can 
I start from?

Thanks,

biohpc

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Re: [gmx-users] cgenff CTAB

[Justin Lemkul]

On 3/29/16 5:40 PM, xy21hb wrote:

Dear all,
I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 
force field in GROMACS.
However, it always gives the wrong error message, saying that the number of 
atoms does not match the .top.
I wonder what could be the reason for this problem.


Usually this means your residue name is specified incorrectly.  Check that your 
command line, .mol2, and RESI specification match.



Attached are .mol2 and .str files.


The list does not accept attachments.  If you need to share files, upload them 
somewhere and provide a URL.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] cgenff CTAB

[xy21hb]

Dear all,
I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 
force field in GROMACS.
However, it always gives the wrong error message, saying that the number of 
atoms does not match the .top.
I wonder what could be the reason for this problem.
Attached are .mol2 and .str files.
 Many thanks,


Yao-- 
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[gmx-users] Gromacs 5.0 Benchmarking Systems

[Benjamin Joseph Coscia]

Good Morning,

I am a graduate student at the University of Colorado at Boulder. The
University is in the process of transitioning to a new supercomputer and
the Research Computing team who is in charge of setting it up said that
they would be happy to benchmark Gromacs on the computer if I provide them
some input files. I could give them some of my own but I think it would be
more beneficial to run the tests using the same systems used to benchmark
Gromacs 5.0 since they are meant to be representative of a variety of
different types of systems.

I read through the documentation which summarized the results of the latest
benchmarking tests but there are no files provided as there are for the
'Old benchmark Suite'. Is there a way that I can access these files for my
own use?

Regards,

Ben Coscia
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Re: [gmx-users] Flat-bottom potential SEGFAULT

[Erik Marklund]

> On 28 Mar 2016, at 01:52, Justin Lemkul  wrote:
> 
> 
> 
> On 3/26/16 12:47 PM, Erik Marklund wrote:
>> Dear dynamicists,
>> 
>> I am using flat bottom potentials to prevent water molecules from 
>> evaporating from a droplet in vacuum. The manual suggests this is pretty 
>> straightforward, but we run into a segfault with our approach. Having never 
>> used flat-bottom potentials before, chances are we are doing something wrong 
>> without realising it. Let me describe what we do and perhaps you can tell me 
>> where things go wrong.
>> 
>> We make our own copy of tip3p.itp, in which we put a [ position_restraints ] 
>> directive for the OW1, HW2, and HW3 atoms:
>> [ position_restraints ]
>> ; id func_typeg   r  k
>> 121   10 1000
>> 221   10 1000
>> 321   10 1000
>> 
>> We then create a new gro-file, where we move all water atoms in the middle 
>> of the box. This is to be used for reference coordinates in the next step.
>> 
>> We run grompp, where we provide the new gro file using the -r flag.
>> 
>> We launch mdrun, which segfaults. If we prepare the system without the -r 
>> flag in the previous step everything runs fins, but the reference point for 
>> the flat-bottom potential is presumably wrong.
>> 
>> Where might the error be?
>> 
> 
> I just did this with a toy system of a single water molecule and it worked 
> quite well.  What version of GROMACS are you using?  Does a simple test like 
> I did work?
> 
> -Justin

Hi,

Forgot to mention the version. It is 5.1.1. Will run some simple tests like 
yours and get back with more info.

Kind regards,
Erik

> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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Re: [gmx-users] Query on g_mmpbsa in gromacs

[rajendra kumar]

Pairwise interaction scheme
 ​
is not implemented in g_mmpbsa. Therefore, g_mmpbsa cannot be used to
calculate interaction energy between two residues.

With best regards,
​Rajendra

​

On Mon, Mar 28, 2016 at 2:37 PM, Prasanna Dr 
wrote:

> Hi
>
> I have been using g_mmpbsa of Rashhmi Kumari and group to calculate binding
> energy of lipids in protein-lipid complex. I got a quite good results with
> g_mmpbsa. Now, In my next step I need to perform network analysis where
> pairwise interaction energy from mmpbsa will be considered.
>
> I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> generated residue decomposition energy of aminoacids with lipid (not
> between aminoacids) as shown below  (for example purpose)
>
> 11.0784
> 2-0.0261
> 30.9493
> 40.0206
> 5-0.0583
> 60.0061
> 7-0.0278
> .
> .
> .
> 450
>
> While running mmpbsa my first input was protein and second input was lipid
> (in place of ligand). Now I have interaction energy of each aminoacid with
> lipid .
>
> Now,  I need interaction energy between aminoacids. like 1st aminoacid with
> remaining 499  aminoacid and 2nd with remaining 499 aminoacids and so on.
>
> Is it possible to calculate interaction energy between amnoacids and with
> lipids using g_mmpbsa (n X n matrix of energy values) ?
>
> --
> D R Prasanna
> Research Scholar
> Computational  Biophysics Group
> Department of Biotechnology
> Indian Institute of Technology Madras
> Chennai
> Tamilnadu-600036
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

[Khuong Truong Gia]

Dear Justin,

I got it. Thank you very much for your kindly reply.

Best regards,
Khuong

On Tue, Mar 29, 2016 at 6:56 PM, Justin Lemkul  wrote:

>
>
> On 3/28/16 9:02 PM, Khuong Truong Gia wrote:
>
>> Dear all,
>>
>> I am running umbrella sampling simulation about binding of a drug
>> (polymer)
>> to a lipid bilayer. Could you please suggest me how can I do
>> position-restraints the reference group (bilayer)? Do I need to restraint
>> all lipid molecules?
>>
>
> You should not have to apply position restraints to anything.
>
> As I read in the gromacs manual there is cylinder option for the
>> pull-geometry, but I am not sure this is suitable for my system or not?
>> Please give me some advice.
>>
>
> Yes, that is a good choice, as the example in the manual is almost
> identical to what you're doing.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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Re: [gmx-users] Query on g_mmpbsa in gromacs

[Justin Lemkul]

On 3/29/16 1:25 AM, Prasanna Dr wrote:

Hi,
Thanks for your quick response.

AMBER mmpbsa does amino-acid pairwise residue decomposition. Pairwise
decomposition energy is very suitable input for weighted network analysis
(to understand the information flow between residues and to find key
amino-acids of a functional protein). I tried to convert gromacs parameters
into AMBER parameters, but I couldn't get success as  I am using modified
force field in gromacs. So values of pairwise residue decomposition is
important for further analysis (Reference:
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b00946). I want do similar
kind of analysis as of reference article using g_mmpbsa (rashmikumari and
group) of gromacs.



There is a help forum for g_mmpbsa that may be more suitable for this question 
(as g_mmpbsa is not an official GROMACS program):


https://groups.google.com/forum/#!forum/g_mmpbsa

-Justin



Hi,

Probably you can find a way to compute a number with this non-GROMACS tool.
But is there any evidence to support that such a number will mean anything?
MM force fields are pairwise additive, not decomposable.

Mark

On Mon, 28 Mar 2016 14:37 Prasanna Dr  wrote:


Hi

I have been using g_mmpbsa of Rashhmi Kumari and group to calculate

binding

energy of lipids in protein-lipid complex. I got a quite good results with
g_mmpbsa. Now, In my next step I need to perform network analysis where
pairwise interaction energy from mmpbsa will be considered.

I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
generated residue decomposition energy of aminoacids with lipid (not
between aminoacids) as shown below  (for example purpose)

11.0784
2-0.0261
30.9493
40.0206
5-0.0583
60.0061
7-0.0278
.
.
.
450

While running mmpbsa my first input was protein and second input was lipid
(in place of ligand). Now I have interaction energy of each aminoacid with
lipid .

Now,  I need interaction energy between aminoacids. like 1st aminoacid

with

remaining 499  aminoacid and 2nd with remaining 449 aminoacids and so on.

Is it possible to calculate interaction energy between amnoacids and with
lipids using g_mmpbsa (n X n matrix of energy values) ?

--
D R Prasanna


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

[Justin Lemkul]

On 3/28/16 9:02 PM, Khuong Truong Gia wrote:

Dear all,

I am running umbrella sampling simulation about binding of a drug (polymer)
to a lipid bilayer. Could you please suggest me how can I do
position-restraints the reference group (bilayer)? Do I need to restraint
all lipid molecules?


You should not have to apply position restraints to anything.


As I read in the gromacs manual there is cylinder option for the
pull-geometry, but I am not sure this is suitable for my system or not?
Please give me some advice.


Yes, that is a good choice, as the example in the manual is almost identical to 
what you're doing.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] maxh mdrun option does not work with REMD simulation

[Maud Jusot]

Dear Gromacs users,

I tried to do a REMD simulation with gromacs 5.1 which is re-launched 
every hour (in a queuing system) with the -maxh option.
The first time it was launched, it worked : the run stoped at the maxh 
time and it was re-launched with the checkpoint files and continued the 
simulation. But during this second run, when the maxh time was achieved 
(step 1981062), gromacs said that it was going to stop but it did not 
stop until the system kill the job (step 2545600) .


I tried with different maxh times ( 1/0.95/0.20 hour) to be sure that 
the time between maxh and the cluster maxtime was sufficient, but in any 
case the second run continued until it reached the one hour and was 
killed by the system.


I find this very strange that it works the first time and that the 
second time gromacs says that it has to stop but does not.
Moreover, I tried the same work but with a classical simulation (without 
REMD) and this time there was no problem.
Did I forget an option or something like that for maxh being compatible 
with the REMD ?
I searched on the web and the mailing list but I did not find any 
recording problems between maxh and REMD.


Do you have any idea of what the problem is ?

Here is the command lines in my script myJob.slurm :
-
srun --mpi=pmi2 -K1 --resv-ports -n $SLURM_NTASKS mdrun_mpi -ntomp 1 
-multi 8 -replex 500 -maxh 0.2 -deffnm mdA_ -cpi mdA_.cpt -cpo mdA_.cpt 
-v 2>> remdA.log

# resubmit the same job at the end for a long run:
sbatch myJob.slurm
-

Here is a part of my remdA.log file :
-
starting mdrun 'myPeptide'
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
starting mdrun 'myPeptide'
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).
12000 steps, 24.0 ps (continuing from step 655701,   1311.4 ps).

Step 1981061: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

Step 1981062: Run time exceeded 0.198 hours, will terminate the run

step 1981100, will finish Sat Mar 26 11:14:40 2016
step 1981200, will finish Sat Mar 26 11:14:40 2016
...
step 2545600, will finish Sat Mar 26 11:15:49 2016srun: Job step 
aborted: Waiting up to 32 seconds for job step to finish.


Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step

Received the TERM signal, stopping at the next NS step
-

Thanks a lot,

Maud





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