Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks again

That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.

Waiting for your suggestion

On Sat, Jan 7, 2017 at 10:35 AM, Amir Zeb  wrote:

> well
> if you are confident of your simulation you may definitly go ahead with
> this ff
> otherwise you will have to change the ff for simulation too
> i think this is not rational to simulate the system with one ff and then
> change the ff for free energy calculations
>
> good luck
>
> On Jan 7, 2017 2:01 PM, "tasneem kausar" 
> wrote:
>
> > Thanks Amir Zeb for your reply
> > I have read in literature about the FEPsetup to parametrize the complex
> > file (protein+drug) for simulation. This setup builds files based on
> amber.
> > Since I have previously used 54a7ff to simulate the protein and drug and
> > topology files were generated from ATB in gromos54a7 format. Since I
> didn't
> > find free energy calculation of protein and ligand with this force field.
> > Thats why I was confused to proceed further using the same.
> >
> > On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <
> tasneemkausa...@gmail.com
> > >
> > wrote:
> >
> > > mm/pbsa calculates binding energy. I have used that.
> > >
> > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
> > >
> > >> hello
> > >> you may use mm/pbsa compiled with gromacs to calculate free energy
> > >> all the best
> > >>
> > >> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> > >> wrote:
> > >>
> > >> > Dear gromacs users
> > >> >
> > >> > It is first time I am trying to perform free energy calculation of
> > >> protein
> > >> > and drug complex. I am following Justin' s tutorial of mehtane in
> > water.
> > >> > That calculation are performed on a neutral system. If the ligand
> > >> molecule
> > >> > has charge what are the provisions that could be taken into account.
> > >> > I have performed my MD simulation using force field gromos54a7. And
> > Now
> > >> I
> > >> > am trying to go onward using free energy calculations. Since the
> free
> > >> > energy calculations are performed on ambed99ldn, opls and charmm
> force
> > >> > fields (as I know from the articles). Is it okay to use gromos54a7
> ff
> > >> for
> > >> > free energy calculations.
> > >> >
> > >> > Kindly tell me
> > >> >
> > >> > Thanks in Advance
> > >> > --
> > >> > Gromacs Users mailing list
> > >> >
> > >> > * Please search the archive at http://www.gromacs.org/
> > >> > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations

good luck

On Jan 7, 2017 2:01 PM, "tasneem kausar"  wrote:

> Thanks Amir Zeb for your reply
> I have read in literature about the FEPsetup to parametrize the complex
> file (protein+drug) for simulation. This setup builds files based on amber.
> Since I have previously used 54a7ff to simulate the protein and drug and
> topology files were generated from ATB in gromos54a7 format. Since I didn't
> find free energy calculation of protein and ligand with this force field.
> Thats why I was confused to proceed further using the same.
>
> On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar  >
> wrote:
>
> > mm/pbsa calculates binding energy. I have used that.
> >
> > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
> >
> >> hello
> >> you may use mm/pbsa compiled with gromacs to calculate free energy
> >> all the best
> >>
> >> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> >> wrote:
> >>
> >> > Dear gromacs users
> >> >
> >> > It is first time I am trying to perform free energy calculation of
> >> protein
> >> > and drug complex. I am following Justin' s tutorial of mehtane in
> water.
> >> > That calculation are performed on a neutral system. If the ligand
> >> molecule
> >> > has charge what are the provisions that could be taken into account.
> >> > I have performed my MD simulation using force field gromos54a7. And
> Now
> >> I
> >> > am trying to go onward using free energy calculations. Since the free
> >> > energy calculations are performed on ambed99ldn, opls and charmm force
> >> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> >> for
> >> > free energy calculations.
> >> >
> >> > Kindly tell me
> >> >
> >> > Thanks in Advance
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
> >> > Support/Mailing_Lists/GMX-Users_List before posting!
> >> >
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> >> >
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
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> >
> >
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromos54a7 format. Since I didn't
find free energy calculation of protein and ligand with this force field.
Thats why I was confused to proceed further using the same.

On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar 
wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
>
>> hello
>> you may use mm/pbsa compiled with gromacs to calculate free energy
>> all the best
>>
>> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
>> wrote:
>>
>> > Dear gromacs users
>> >
>> > It is first time I am trying to perform free energy calculation of
>> protein
>> > and drug complex. I am following Justin' s tutorial of mehtane in water.
>> > That calculation are performed on a neutral system. If the ligand
>> molecule
>> > has charge what are the provisions that could be taken into account.
>> > I have performed my MD simulation using force field gromos54a7. And Now
>> I
>> > am trying to go onward using free energy calculations. Since the free
>> > energy calculations are performed on ambed99ldn, opls and charmm force
>> > fields (as I know from the articles). Is it okay to use gromos54a7 ff
>> for
>> > free energy calculations.
>> >
>> > Kindly tell me
>> >
>> > Thanks in Advance
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
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>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
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>>
>
>
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?

On Jan 7, 2017 1:38 PM, "tasneem kausar"  wrote:

> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:
>
> > hello
> > you may use mm/pbsa compiled with gromacs to calculate free energy
> > all the best
> >
> > On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> > wrote:
> >
> > > Dear gromacs users
> > >
> > > It is first time I am trying to perform free energy calculation of
> > protein
> > > and drug complex. I am following Justin' s tutorial of mehtane in
> water.
> > > That calculation are performed on a neutral system. If the ligand
> > molecule
> > > has charge what are the provisions that could be taken into account.
> > > I have performed my MD simulation using force field gromos54a7. And
> Now I
> > > am trying to go onward using free energy calculations. Since the free
> > > energy calculations are performed on ambed99ldn, opls and charmm force
> > > fields (as I know from the articles). Is it okay to use gromos54a7 ff
> for
> > > free energy calculations.
> > >
> > > Kindly tell me
> > >
> > > Thanks in Advance
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

mm/pbsa calculates binding energy. I have used that.

On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb  wrote:

> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar" 
> wrote:
>
> > Dear gromacs users
> >
> > It is first time I am trying to perform free energy calculation of
> protein
> > and drug complex. I am following Justin' s tutorial of mehtane in water.
> > That calculation are performed on a neutral system. If the ligand
> molecule
> > has charge what are the provisions that could be taken into account.
> > I have performed my MD simulation using force field gromos54a7. And Now I
> > am trying to go onward using free energy calculations. Since the free
> > energy calculations are performed on ambed99ldn, opls and charmm force
> > fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> > free energy calculations.
> >
> > Kindly tell me
> >
> > Thanks in Advance
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

hello
you may use mm/pbsa compiled with gromacs to calculate free energy
all the best

On Jan 7, 2017 1:27 PM, "tasneem kausar"  wrote:

> Dear gromacs users
>
> It is first time I am trying to perform free energy calculation of protein
> and drug complex. I am following Justin' s tutorial of mehtane in water.
> That calculation are performed on a neutral system. If the ligand molecule
> has charge what are the provisions that could be taken into account.
> I have performed my MD simulation using force field gromos54a7. And Now I
> am trying to go onward using free energy calculations. Since the free
> energy calculations are performed on ambed99ldn, opls and charmm force
> fields (as I know from the articles). Is it okay to use gromos54a7 ff for
> free energy calculations.
>
> Kindly tell me
>
> Thanks in Advance
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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[gmx-users] Free energy calculation of protein and drug

[tasneem kausar]

Dear gromacs users

It is first time I am trying to perform free energy calculation of protein
and drug complex. I am following Justin' s tutorial of mehtane in water.
That calculation are performed on a neutral system. If the ligand molecule
has charge what are the provisions that could be taken into account.
I have performed my MD simulation using force field gromos54a7. And Now I
am trying to go onward using free energy calculations. Since the free
energy calculations are performed on ambed99ldn, opls and charmm force
fields (as I know from the articles). Is it okay to use gromos54a7 ff for
free energy calculations.

Kindly tell me

Thanks in Advance
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Re: [gmx-users] Specs for GPU box

[Alex]

Hi Szilárd,

Thanks for responding. Yes, those systems are indeed expensive, and our 
main objective here wasn't really bang for the buck. What we want is the 
fastest possible single node for the money, and if that means an extra 
$5-10K, we're okay with that. The machine we want to build isn't 
dedicated to MD, but more of a general purpose number crunching beast.  
For DFT calculations we want what you described, i.e. 1-2TB --  these 
benefit tremendously from massive amounts of RAM and CPU clock rate & 
cache amount. So, we want a _really_ fast machine, which among other 
things will perform beautifully with GMX and LAMMPS. Yes, the K80 cards 
appear to be well outdated for our CPU selection. What would you 
recommend in terms of GPUs for an E7-based system?


We will be working with a vendor, who, given the amount of money in 
question, will likely agree to assemble the machine and do benchmarks 
prior to sale. Given what you said already, can you suggest any GPUs to 
start with? If you guys are interested, I am 100% open to sharing the 
benchmark results.


Thank you!

Alex


On 1/6/2017 6:05 AM, Szilárd Páll wrote:

Hi Alex,

Benchmarks of quad-socket Intel machines are rare because AFAIK such
systems are mighty expensive and you will not get good bang for buck with
them, especially if you combine these pricey nodes/CPUs with the old and
slow K80s.

The only reason to get E7 is if >=4 sockets or >1.5 TB memory per node is a
must. Furthermore, the only reason to buy K80s today (for GROMACS) if they
are dirt-cheap (e.g. free :).

You'll be much better off with:
- 1-2-socket Broadwell nodes
- P100 if you need Tesla, GeForce 1070/1080

However, more importantly, what kind of simulations you want to run? For
50K you might be able to get multiple nodes with optimal price/perf.

Cheers,
--
Szilárd

On Tue, Dec 27, 2016 at 9:24 PM, Alex  wrote:


Hi all,

We've got some dedicated funding (~50K) for a computing box. GMX will be
one of the applications used there (the other MD package would be LAMMPS,
which has similar requirements). Other applications would be ab initio and
DFT packages, so, aside from a ton of RAM and possibly a fast SSD for
scratch, there aren't too many requirements.

My question is about an "optimal" CPU-GPU combination. Initially, we wanted
something like a quad-Xeon (something relatively senior in the E7 family,
~48-64 cores total) with two K80 cards, but I can't find anything like this
in your benchmark documents.

Can someone help spec this thing?

Thanks a lot,

Alex
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Re: [gmx-users] Gromacs Simulation Question

[Zheng Ruan]

Hi,

You find find this paper relevant (
https://www.ncbi.nlm.nih.gov/pubmed/22034434).

Ruan

On Fri, Jan 6, 2017 at 5:14 PM, Academic Research 
wrote:

> Hello everyone,
>
>
> I have computationally designed several synthetic proteins that are not
> found in nature.
>
>
> My lab has limited resources for wet lab work and so I would like to use
> gromacs to simulate these proteins in water and see weather they unfold or
> aggregate. I know the best way is to actually express and purify these
> proteins and observe them, but my idea is to use molecular simulation to
> screen through these designed proteins and priorities the ones that appear
> not to unfold nor aggregate.
>
>
> 1. From your experiences, does my idea sound so crazy that I should
> abandon it?
>
>
> 2. Does the Lysozyme in water tutorial from the Bevan Lab a good starting
> point?
>
>
> 3. Are there existing tutorials or papers that simulate protein unfolding
> or aggregation that I could use as a starting point?
>
>
> Much appreciated,
>
>
> AC Research
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[gmx-users] Gromacs Simulation Question

[Academic Research]

Hello everyone,


I have computationally designed several synthetic proteins that are not found 
in nature.


My lab has limited resources for wet lab work and so I would like to use 
gromacs to simulate these proteins in water and see weather they unfold or 
aggregate. I know the best way is to actually express and purify these proteins 
and observe them, but my idea is to use molecular simulation to screen through 
these designed proteins and priorities the ones that appear not to unfold nor 
aggregate.


1. From your experiences, does my idea sound so crazy that I should abandon it?


2. Does the Lysozyme in water tutorial from the Bevan Lab a good starting point?


3. Are there existing tutorials or papers that simulate protein unfolding or 
aggregation that I could use as a starting point?


Much appreciated,


AC Research
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Re: [gmx-users] Fix the residues

[Justin Lemkul]

On 1/6/17 2:41 PM, liming_52 wrote:

Thank you for reppy. The full information is as follows:
$ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS:  gmx pdb2gmx, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin//gmx.exe
Data prefix:  /usr/local/gromacs
Command line:
  gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce

Select the Force Field:
From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
9
Using the Gromos43a1 force field in directory gromos43a1.ff
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.r2b
Reading lactoferrin.pdb...
WARNING: all CONECT records are ignored
Read 2560 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 335 residues with 2560 atoms
  chain  #res #atoms
  1 'A'   335   2560
All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/atomtypes.atp
Atomtype 50
Reading residue database... (gromos43a1)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.rtp
Residue 96
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 'A' (2560 atoms, 335 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 500 donors and 499 acceptors were found.
There are 743 hydrogen bonds
Will use HISE for residue 420
Will use HISH for residue 458
Will use HISD for residue 588
Will use HISE for residue 595
Will use HISE for residue 606
Will use HISE for residue 613
Identified residue TYR342 as a starting terminus.
Identified residue SER676 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
  CYS348  CYS358  CYS371  CYS380  CYS405  HIS420  CYS425
SG64   SG138   SG241   SG300   SG481  NE2595   SG629
  CYS358   SG138   0.849
  CYS371   SG241   0.940   0.213
  CYS380   SG300   0.204   0.933   1.049
  CYS405   SG481   1.411   2.186   2.303   1.371
  HIS420  NE2595   3.406   3.321   3.509   3.348   3.338
  CYS425   SG629   2.460   2.150   2.323   2.429   2.901   1.313
  CYS457   SG875   2.702   2.932   3.096   2.502   2.930   3.532   3.094
  

Re: [gmx-users] replica exchange: checkpoint file not getting generated

[shivangi nangia]

Hi Mark,

Thanks.

Things work fine with Gromacs 2016.

Thanks,
Sxn

On Dec 12, 2016 4:49 PM, "Mark Abraham"  wrote:

> Hi,
>
> We periodically hear reports of people unable to checkpoint reliably with
> some forms of replica exchange, but no clear pattern has emerged, and
> nobody has yet shared a set of inputs that reproduce. If you can reproduce
> it with GROMACS 2016, please open an issue at https://redmine.gromacs.org
> and
> share your input files and perhaps we can find a problem to fix.
>
> Mark
>
> On Tue, Dec 13, 2016 at 5:56 AM shivangi nangia  >
> wrote:
>
> > Hi,
> >
> > I am carrying out replica exchange solute tempering (REST) using the FEP
> > module.
> >
> > For some reason on continuing my simulations, the .cpt file is not
> getting
> > generated.
> >
> > I am confused why this might be happening as for the first run .cpt files
> > did get generated (so no possible mistake of -cpt being set to -1).
> >
> >
> > *The output options in my .mdp file are:*
> >
> > ; Output control
> >
> > nstxout  = 500
> >
> > nstvout  = 500
> >
> > nstfout  = 0
> >
> > nstlog   = 500
> >
> > nstenergy= 500
> >
> >
> > *Commands that I am using:*
> >
> > set HOST = `hostname`
> >
> > set USER = `whoami`
> >
> > set indir=$SLURM_SUBMIT_DIR
> >
> > set workdir = $indir/$SLURM_JOB_ID
> >
> > set tpr = 2run
> >
> > set cptin = /shared/replica_exchange/solute_tempering/1run/1runcpt
> >
> > set outdir = $indir
> >
> > set outname = 2run
> >
> > set cpot = 2runcpt
> >
> >
> > srun  gmx_mpi mdrun  -s $tpr -deffnm $outname -cpi $cptin -multi 11
> > -replex 500 -dhdl dhdl_2run -cpo $cpot
> >
> >
> > I have also tried changing the default .cpt writing time from 15 minutes
> to
> > 1 minute by using the flag -cpt 1, the checkpoint file still does not get
> > generated.
> >
> > srun  gmx_mpi mdrun  -s $tpr -deffnm $outname -cpi $cptin -multi 11
> > -replex 500 -dhdl dhdl_2run -cpo $cpot -cpt 1
> >
> > I could not find any previous dicussions regarding such a problem.
> >
> > Kindly suggest.
> >
> > Thanks,
> > sxn
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
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Re: [gmx-users] window spacing in umbrella sampling

[Justin Lemkul]

On 1/6/17 2:22 PM, faride badalkhani wrote:

Dear GROMACS users,

I have performed pulling simulations on polymer-drug complex an each window
was obtained by an increment of 1 Å from the previous window, and for each
window, 5 ns MD simulation was performed. But the histogram for the first 6
windows is as follows:

https://www.dropbox.com/s/2yzmbyl2nrt6hwq/histo.xlsx?dl=0

I am very beginner in Umbrella sampling. Could you tell me how should I
change the sampling to get a reasonable histogram, please?



The windows are not evenly spaced and/or the force constant is insufficient to 
maintain the desired restraint distances.  You have mostly redundant windows 
with a huge gap.  You may need more windows, better/different spacing, and/or 
different force constants.


-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] Farideh Khamseh shared "histo.xlsx" with you

[Farideh Khamseh (via Dropbox)]

Hi there,

Farideh Khamseh (farideh.kham...@gmail.com) invited you to view the file " 
histo.xlsx " on Dropbox.

View file[1]

Enjoy!
The Dropbox team

[1]: https://www.dropbox.com/l/scl/AAAtNLZS5tTOC0kssvnl8e0ms-GkfMQbWEw
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Re: [gmx-users] Fix the residues

[Justin Lemkul]

On 1/6/17 1:58 PM, liming_52 wrote:

Dear Gromacs users,

I am trying to run a md using 4n6p.cif, which was obtained from PDB. I 
converted the file into pdb format using DS4.1, and got the file named 
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", 
the program runs and produces the information as follows:
...


You snipped out the most important information.  Please provide the full screen 
output from pdb2gmx.


-Justin


WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 335 named SER of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

...
How should I fix the residues? And which tools should I use? Is there any 
examples or tutorials?

If anyone can suggest a solution to this issue, it would be really helpful.







--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



--
==

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] window spacing in umbrella sampling

[faride badalkhani]

Dear GROMACS users,

I have performed pulling simulations on polymer-drug complex an each window
was obtained by an increment of 1 Å from the previous window, and for each
window, 5 ns MD simulation was performed. But the histogram for the first 6
windows is as follows:

https://www.dropbox.com/s/2yzmbyl2nrt6hwq/histo.xlsx?dl=0

I am very beginner in Umbrella sampling. Could you tell me how should I
change the sampling to get a reasonable histogram, please?

Regards,
F.
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[gmx-users] Farideh Khamseh shared "histo.xlsx" with you

[Farideh Khamseh (via Dropbox)]

Hi there,

Farideh Khamseh (farideh.kham...@gmail.com) invited you to view the file " 
histo.xlsx " on Dropbox.

View file[1]

Enjoy!
The Dropbox team

[1]: https://www.dropbox.com/l/scl/AABx-njEs4l7Xh-vbDVRhAm9tmezAB5fXO0
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[gmx-users] Fix the residues

[liming_52]

Dear Gromacs users,

I am trying to run a md using 4n6p.cif, which was obtained from PDB. I 
converted the file into pdb format using DS4.1, and got the file named 
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce", 
the program runs and produces the information as follows:
...
WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
 
WARNING: WARNING: Residue 335 named SER of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

...
How should I fix the residues? And which tools should I use? Is there any 
examples or tutorials?

If anyone can suggest a solution to this issue, it would be really helpful.







--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
-- 
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Re: [gmx-users] Save the velocities a subset of atoms in a trr file during a simulation

[Justin Lemkul]

On 1/6/17 1:34 PM, ABEL Stephane 175950 wrote:

ello,

A quick question :

It is possible to save the velocities (in a trr file) for only selected atoms 
"during" a simulation as we can do in case of  the xtc files by using a the mdp 
option compressed-x-grps?



No.

If storage is an issue, run jobs in short chunks of time, extract velocities for 
the atoms of interest, throw away the bulky file, and continue without appending.


-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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Re: [gmx-users] Regarding gromacs commands..

[Justin Lemkul]

On 1/6/17 2:24 AM, Dilip H N wrote:

no...
I want to create  300 molecules of ammonia...


Well, you asked about BF3, so you got an answer about BF3 :)


how can i create  300 molecules of ammonia and then get it in .pdb file
format..??



For a simple molecule like NH3 you can easily write the coordinates by hand from 
basic geometry.  Otherwise, find an NMR structure of a protein that contains Lys 
and copy its NZ-HZ[123] group and use that.  gmx insert-molecules -nmol 300 will 
give you a box of 300.


-Justin




 Sent with Mailtrack


On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:


Google "bf3 rcsb" > third result from the top
https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
the right) > open in pymol > save as pdb

Alex


On 1/5/2017 10:20 PM, Dilip H N wrote:


I want to do a simulation of BF3 molecule..
how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??




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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] Index file group selection and gmx covar error

[Justin Lemkul]

On 1/5/17 3:40 AM, Aditya Padhi wrote:

Dear Gromacs users,

I am trying to evaluate entropic contributions for a protein-protein
complex using the gmx covar module and then gmx anaeig. When I directly run
the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
-v eigenval.trr -av average.pdb -l covar.log", the program runs and
produces the output. However, when I try to submit it into a node having 16
cores, it shows "Illegal instruction" error and it doesn't run.



This usually means the binary is compiled in a manner that is not compatible 
with the target hardware (e.g. the machine where you compiled GROMACS is 
different than the compute node).



In addition, when I use "qsub" to submit the job into the particular node,
it tries to run but eventually I get an error "Fatal error: No input files
(structure or index)". I was wondering if there is any way to specify my
group selection (for e.g. 18 and 19) directly in my input.sh file when I
submit using qsub and is it sufficient to make this run successful? Or the
problem is something related to the pre-compiled binaries.



http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-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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Re: [gmx-users] How can I calculate Potential Energy of the segment divided by index file?

[Justin Lemkul]

On 1/5/17 3:58 PM, 大木啓輔 wrote:

Dear Gromacs users


I want to calculate Potential Energy of segment of the structure.
For example, segment that coordinations in z axis are 7.2 Å in the structure.

I could specify that segment of atom numbers by writing index file.
But gmx energy has no option of specifying segments by index file.

Then, how should I get the Potential Energy of segments?
Could you tell me how to solve this problem, please?



You can create an index file with gmx select, extract those coordinates from the 
trajectory, create a matching .tpr file with convert-tpr, then use mdrun -rerun 
to recalculate the energies.  I'm not sure what use those values will be, but 
that's how you'd compute them.


-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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Re: [gmx-users] Protein-complex simulation

[Justin Lemkul]

On 1/6/17 1:58 AM, Nivedita Rai wrote:

Dear gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?



If you are using cutoff-scheme = Verlet, it is meaningless because charge groups 
are ignored (and this method is preferred).  If not, find that charge group and 
figure out if it is right because neighbor searching can be affected by charge 
groups that are too large.


-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] Save the velocities a subset of atoms in a trr file during a simulation

[ABEL Stephane 175950]

ello, 

A quick question : 

It is possible to save the velocities (in a trr file) for only selected atoms 
"during" a simulation as we can do in case of  the xtc files by using a the mdp 
option compressed-x-grps?   

Thanks

S
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[gmx-users] Simulated Tempering Issues

[Alexander Yang]

Dear Gromacs users,

I've been attempting simulated tempering (ST) in Gromacs to study gel-phase
bilayers (~15000 atoms), but I've been encountering some difficulties. I've
been following similar steps in the expanded ensemble tutorial on
alchemistry.org and adapting them for ST. The system I am studying is
already fairly well-equilibrated, so I don't imagine any huge movements in
the system.

I've picked very modest temperature values (305 K - 350 K with 2.5 K
spacing), yet I've been getting domain decomposition errors upon restarting
the simulation. I've done brief simulations (same MD parameters) on
clusters for 15 minutes and 30 minutes without crashing. When continuing
either simulation, the system crashes and throws the domain decomp error.
On the other hand, running these simulations indefinitely on the head node
does not exhibit crashes at the steps that have crashed for restarts after
15 minutes. I'm not sure if this is a coincidence with a ST move error, an
error with my MD parameters, or something with restarts. Could someone
advise? I've copied the error, last few lines of the log, and mdp below.

Error

Fatal error:

An atom moved too far between two domain decomposition steps

This usually means that your system is not well equilibrated

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors



-Log---
DD  step 3854999  vol min/aver 0.401  load imb.: force 11.2%  pme
mesh/force 2.059


   Step   Time Lambda

3855000 7710.00.0


   Energies (kJ/mol)

G96Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)

1.31304e+041.57687e+049.63926e+037.34404e+02   -9.18268e+03

  Disper. corr.   Coulomb (SR)   Coul. recip.  PotentialKinetic En.

   -2.70660e+03   -2.50854e+051.12235e+03   -2.22348e+055.38027e+04

   Total EnergyTemperature Pres. DC (bar) Pressure (bar)

   -1.68545e+053.58572e+02   -1.70205e+02   -2.93216e+02


DD  step 385  vol min/aver 0.391  load imb.: force  7.7%  pme
mesh/force 2.344


   Step   Time Lambda

386 7720.00.0


 MC-lambda information

  Wang-Landau incrementor is:   1

  N  Temp.(K)Count   G(in kT)  dG(in kT)

  1  305.000  1930.0  193.0

  2  307.5000  193.00.0

  3  310.0000  193.00.0

  4  312.5000  193.00.0

  5  315.0000  193.00.0

  6  317.5000  193.00.0

  7  320.0000  193.00.0

  8  322.5000  193.00.0

  9  325.0000  193.0  -35.0

 10  327.500   35  158.0  -96.0

 11  330.000  131   62.0  -95.0

 12  332.500  226  -33.0  -95.0

 13  335.000  321 -128.0  -95.0

 14  337.500  416 -223.0  -95.0

 15  340.000  511 -318.0  -95.0

 16  342.500  606 -413.0  -97.0

 17  345.000  703 -510.0  -93.0

 18  347.500  796 -603.0  -91.0 <<

 19  350.000  887 -694.00.0


   Energies (kJ/mol)

G96Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)

1.24610e+041.60933e+049.86938e+037.51926e+02   -8.56113e+03

  Disper. corr.   Coulomb (SR)   Coul. recip.  PotentialKinetic En.

   -2.69740e+03   -2.52430e+051.08555e+03   -2.23427e+055.48813e+04

   Total EnergyTemperature Pres. DC (bar) Pressure (bar)

   -1.68546e+053.65761e+02   -1.69051e+023.42231e+02


DD  step 3864999  vol min/aver 0.397  load imb.: force  9.8%  pme
mesh/force 1.822


   Step   Time Lambda

3865000 7730.00.0


   Energies (kJ/mol)

G96Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)

1.33244e+041.56493e+049.63355e+037.38294e+02   -7.52212e+03

  Disper. corr.   Coulomb (SR)   Coul. recip.  PotentialKinetic En.

   -2.67952e+03   -2.52827e+051.16878e+03   -2.22514e+055.50394e+04

   Total EnergyTemperature Pres. DC (bar) Pressure (bar)

   -1.67475e+053.66815e+02   -1.66819e+025.74291e+02


+04

   Total EnergyTemperature Pres. DC (bar) Pressure (bar)

   -1.71349e+053.54322e+02   -1.63023e+02   -7.17865e+00




MDP--
;title   = Simulated Tempering Run

; Run parameters

integrator  = md-vv

nsteps  = 2500 ; 50ns

dt  = 0.002


; Output control

nstxout = 0 ; Don't save coordinates

nstvout = 0 ; Don't save velocities

nstenergy   = 5000

nstlog  = 5000

nstxtcout   = 5000


;bond parameters

continuation= yes

[gmx-users] PMF simulation in Gromacs 2016.1

[Li, Shi]

Dear Gromacs users,

I am comparing the PMF simulations using the Gromacs 2016 version with old
version 5.0.5. I found the *gmx wham* in Gromacs 5.0.5 couldn't process the
tpr files generated by Gromacs 2016.1 . (tpx version 100 vs. tpx version
110). The new Gromacs 2016.1 can process the tpr files that generated from
Gromacs 5.0.5, but the results are different, most of the energy in the new
output .xvg file is zero, but using the old version to process the same
input files, the resulting .xvg is fine.

While using the Gromacs 2016.1 to process the tpx version 110
files(generated by the new version). The resulting .xvg also shows a lot of
zero energies.

I am not sure where I did wrong or how to fix this problem, any suggestion
will be appreciated.

Thanks.
Shi
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Re: [gmx-users] Continuing a FEP alchemical

[Alex]

Dear Hannes,

Yes, I mean David Mobley's tool.
I checked it out, however it crashed exactly in the *.xvg file (prd.15.xvg
and afterward) in which additional \lambada getting involved. I invoked
below command to get rid of other method except TI:

"alchemical_analysis -p prd. -u kcal -f 20 -o 100dis -s 100 -c -g -v -m
'-ti_cubic-dexp-iexp-bar-mbar' -i 10",


Traceback (most recent call last):
  File "/usr/bin/alchemical_analysis", line 9, in 
load_entry_point('alchemical-analysis==1.0.2.dev0', 'console_scripts',
'alchemical_analysis')()
  File "/usr/lib/python2.7/site-packages/alchemical_analysis-
1.0.2.dev0-py2.7.egg/alchemical_analysis/alchemical_analysis.py", line
1207, in main
nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
  File "/usr/lib/python2.7/site-packages/alchemical_analysis-
1.0.2.dev0-py2.7.egg/alchemical_analysis/parser_gromacs.py", line 308, in
readDataGromacs
nsnapshots[nf,nf] += unixlike.wcPy(f.filename) - f.skip_lines -
1*bLenConsistency
IndexError: index 15 is out of bounds for axis 1 with size 15

Thanks.

Best regards,
Alex


On Wed, Dec 28, 2016 at 5:38 PM, Hannes Loeffler  wrote:

> On Wed, 28 Dec 2016 17:24:08 +0100
> Alex  wrote:
>
> > Thank for your response.
> >
> > You mean for the TI analysis, now problem if one .xvg file (e.g.
> > case.3.xvg) has just 15 columns while another .xvg file (e.g.
> > case.18.xvg) has 20 columns? and still the "alchemical analysis
> > package" could be used to calculate the free energy change via TI
> > method?
>
> I suppose you mean David Mobley's tool.  Yes, it can do that.  You can
> easily check that yourself though.
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Re: [gmx-users] Specs for GPU box

[Szilárd Páll]

Hi Alex,

Benchmarks of quad-socket Intel machines are rare because AFAIK such
systems are mighty expensive and you will not get good bang for buck with
them, especially if you combine these pricey nodes/CPUs with the old and
slow K80s.

The only reason to get E7 is if >=4 sockets or >1.5 TB memory per node is a
must. Furthermore, the only reason to buy K80s today (for GROMACS) if they
are dirt-cheap (e.g. free :).

You'll be much better off with:
- 1-2-socket Broadwell nodes
- P100 if you need Tesla, GeForce 1070/1080

However, more importantly, what kind of simulations you want to run? For
50K you might be able to get multiple nodes with optimal price/perf.

Cheers,
--
Szilárd

On Tue, Dec 27, 2016 at 9:24 PM, Alex  wrote:

> Hi all,
>
> We've got some dedicated funding (~50K) for a computing box. GMX will be
> one of the applications used there (the other MD package would be LAMMPS,
> which has similar requirements). Other applications would be ab initio and
> DFT packages, so, aside from a ton of RAM and possibly a fast SSD for
> scratch, there aren't too many requirements.
>
> My question is about an "optimal" CPU-GPU combination. Initially, we wanted
> something like a quad-Xeon (something relatively senior in the E7 family,
> ~48-64 cores total) with two K80 cards, but I can't find anything like this
> in your benchmark documents.
>
> Can someone help spec this thing?
>
> Thanks a lot,
>
> Alex
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Re: [gmx-users] HOW TO RUN GROMACS IN WINDOWS 7

[Szilárd Páll]

On Fri, Jan 6, 2017 at 8:21 AM, Subashini .K  wrote:
> Hi Gromacs users,
>
>
> I am new to Gromacs. Have installed it in windows 7.
>
> Had followed the instructions this website 
> https://winmostar.com/en/gmx4wm_en_win.html
>
>
> How to run a test file through cygwin? Can someone help?

What do you mean by that? Have run ran the tests?
http://manual.gromacs.org/documentation/2016.1/install-guide/index.html#testing-gromacs-for-correctness

--
Szilárd

>
>
> Thanks,
>
> Subashini.K
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Re: [gmx-users] generation of ions additional to solvent molecules

[Erik Marklund]

Dear Raag,

Where would those extra ions go? If you need a higher number density of ions 
than the solvent (assuming the box is full of water, plus the protein) you will 
most likely raise the pressure of the system to bizarre levels. What ion 
concentration are you aiming for? Is that a reasonable concentration?

Kind regards,
Erik

> On 6 Jan 2017, at 07:05, Raag Saluja  wrote:
> 
> Hi!
> 
> I wanted to study the impact of certain ions on a particular protein.
> Earlier, I used to simply replace the solvent molecules with the ions.
> However, in the current case I need to add a very large number of ions,
> which exceeds the number of solvent molecules.So its giving me an error.
> 
> The command I used was:
> 
> genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np
> 84300
> 
> Is there a way to add ions additional to the solvent molecules, instead of
> replacing them?
> 
> Thank you and regards,
> 
> Raag Saluja
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