Re: [gmx-users] problem: gromacs run on gpu

[Alex]

Can you try to open the script in vi, delete the mdrun line and then 
manually retype it?



On 7/12/2017 11:03 PM, leila karami wrote:

Dear Gromacs users,

I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using
command:

gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on

All things are ok.

When I use this command in a script to do md simulation by queuing system:

-
#!/bin/bash
#$ -S /bin/bash
#$ -q gpu.q
#$ -cwd
#$ -N cell_1
#$ -e error_1.dat
#$ -o output_1.dat
echo "Job started at date"
gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
echo "Job Ended at date"
-

I encountered with following error:

Program: gmx mdrun, VERSION 5.1.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
   In command-line option -pin
 Invalid value: on

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Halting program gmx mdrun
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

---

How to resolve this error?
Any help will be highly appreciated


--
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.

[gmx-users] problem: gromacs run on gpu

[leila karami]

Dear Gromacs users,

I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using
command:

gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on

All things are ok.

When I use this command in a script to do md simulation by queuing system:

-
#!/bin/bash
#$ -S /bin/bash
#$ -q gpu.q
#$ -cwd
#$ -N cell_1
#$ -e error_1.dat
#$ -o output_1.dat
echo "Job started at date"
gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
echo "Job Ended at date"
-

I encountered with following error:

Program: gmx mdrun, VERSION 5.1.3
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -pin
Invalid value: on

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Halting program gmx mdrun
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

---

How to resolve this error?
Any help will be highly appreciated
-- 
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.

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Alex]

I wonder if the "couple-intramol = yes" is a must. Does it have any 
influence on the output results if we turn off the intra-molecular 
non-bonded interactions of a large infinite molecule?


The answer to your question has nothing to do with Gromacs, but with 
understanding the difference between crystals and biomolecules (for 
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes 
something infinite -- the effective size of your system is entirely 
determined by the supercell size (proof: consider the ripples in hBN and 
determine the lowest wavelength of the ripple that can propagate -- it 
is commensurate with the box size). In an infinite system, you can have 
an immensely long wave (though not infinite, as shown by Landau a while 
back). PBC does not make anything infinite, it is a mathematical way of 
avoiding surfaces.


There is no universal force field for HBN, so I am using a modified 
gromos54a7_atb force field, i.e., manually adding the parameters for 
boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My 
question was about which Gromacs ff you were using to insert your 
parameters, and, most importantly, where those parameters came from.



The parameters are obtained from literature.

What literature? All bio-style ff adaptations of solid-state potentials 
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that 
"intramolecular" interactions between atoms sharing up to a fairly 
distant covalently bound neighbor are limited to bonds and angles. This 
comes from the math involved in developing potentials for crystals. 
There was a recent question regarding this very problem here, which was 
solved by setting a larger nrexcl value. In your case, you solved it 
with turning off intramolecular coupling. In fact, if you set your 
nrexcl to something like 4 or 5, you may not even need to turn off the 
coupling. But then again, I don't know where the parameters came from.


Alex
--
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.

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Jason Zhu]

Hi Alex,

Thank you for your reply. Here below is my response to your comments.


hBN is hardly a common subject of simulation for Gromacs folks, but let's
see...

1. When you run the simulation in vacuum, do you get the same error?
Does a 300K vacuum simulation result in reasonable sheet behavior? What
about NVT?


The answer is yes. I ran more tests today, and I think I have found exactly
how the error came out.
In fact, if I remove the whole free energy calculation section from my mdp
file, the system will run perfectly in parallel, both HBN in vacuum and HBN
in solution.
So I suspect somewhere in FEC section is causing the trouble.
Then I looked up each command in GROMACS documentation, and found this
"couple-intramol" flag:

"couple-intramol:
no
All intra-molecular non-bonded interactions for moleculetype couple-moltype
are replaced by exclusions and explicit pair interactions. In this manner
the decoupled state of the molecule corresponds to the proper vacuum state
without periodicity effects.
yes
The intra-molecular Van der Waals and Coulomb interactions are also turned
on/off. This can be useful for partitioning free-energies of relatively
large molecules, where the intra-molecular non-bonded interactions might
lead to kinetically trapped vacuum conformations. The 1-4 pair interactions
are not turned off."

I wonder if the "couple-intramol = no" works periodic molecules.

In my mdp file, I set the flag to "no", because both reference tutorials
set it to "no".
However, I am dealing with a relative large molecule with periodicity, so I
should have set this flag to "yes".

Then I ran several more test with "couple-intramol = yes". Now, for
EM/NVT/NPT/PROD_MD, the system could finally run in parallel. No more
disturbing errors. Hooray!!

But I am still confused about the setting of "couple-intramol". Why it can
run parallelly if "couple-intramol" is set "yes". The hBN sheet in my
simulation is infinite with PBC.

I wonder if the "couple-intramol = yes" is a must. Does it have any
influence on the output results if we turn off the intra-molecular
non-bonded interactions of a large infinite molecule?

Please note that "periodic-molecules = yes" in all my simulations.


2. What GROMACS forcefield are you using and what are the nonbonded
types for boron and nitrogen?


There is no universal force field for HBN, so I am using a modified
gromos54a7_atb force field, i.e., manually adding the parameters for boron
and nitrogen to the bonded & nonbonded .itp files.
The parameters are obtained from literature.

 
3. How was the topology obtained? If x2top was used, was the BN sample
in a box with in-plane PBC?


I did use x2top to generate the topology of hBN sheet by using the
following command:

g_x2top_mpi -f HBN-z-2.gro -o hbn-x2top.top -ff bnt_oplsaa -name BNT
-noparam -pbc -alldih

PBC is considered here. And some additional modifications are carried out
manually.


Best,
Xuliang
-- 
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.

Re: [gmx-users] gmx select

[Mark Abraham]

Hi,

Can you please copy, paste and post your actual commands. I don't think
your use of quote marks would have led to a valid shell command. The whole
selection text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash  wrote:

> I have used the same name in my coordinate file. For Glycine it is spelt
> as Glyci, so the word has been cut off. I know this is correct because I
> use the same name in VMD.
>
> -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: 12 July 2017 22:42
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably doesn't
> fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci and
> > within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file)
> > -select "Close to protein" resname Glyci and within 0.5 of group
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me with
> this?
> >
> >
> > Akash
> > --
> > 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.
> >
> --
> 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.
> --
> 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.
>
-- 
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.

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

[Szilárd Páll]

Additionally, if you care about getting the best performance on your
hardware be aware that distro-packaged GROMACS versions are generally
optimized for the lowest common denominator CPU architectural capabilities
and will not be able to make the best use of modern CPU instructions sets.
Hence, if performance matter for you, do compile from source.

For more details see:
http://manual.gromacs.org/documentation/2016.3/install-guide/index.html#simd-support

--
Szilárd

On Wed, Jul 12, 2017 at 5:51 PM, Jose Borreguero 
wrote:

> will do, thanks for the tip.
>
> On Wed, Jul 12, 2017 at 11:42 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > That kind of information is in the release notes, e.g. at
> > http://manual.gromacs.org/documentation/. Perhaps you want to start with
> > the 2016 ones :-)
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero 
> > wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I'm a relatively new user of Gromacs and recently realized there is a
> > > "2016" branch that is still being updated. What is the difference with
> > the
> > > 5.x branch?
> > >
> > > I ask because I could find RPM packages only for the 2016 version, much
> > > easier to install than building from source.
> > >
> > > Best,
> > > .Jose
> > > --
> > > 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] gmx select

[Pandya, Akash]

I have used the same name in my coordinate file. For Glycine it is spelt as 
Glyci, so the word has been cut off. I know this is correct because I use the 
same name in VMD.   

-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: 12 July 2017 22:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

What are the residue names in your coordinate file? Glyci probably doesn't fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
wrote:

> Hi all,
>
>
> I am trying to select all the glycine molecules with 0.5nm of my protein.
> I tried both of these commands I got from the gromacs website:
>
> gmx select -f output.gro -select "Close to protein" resname Glyci and 
> within 0.5 of group "Protein"' -ofpdb
>
> gmx select -f output.xtc -s output.tpr (my converted input file) 
> -select "Close to protein" resname Glyci and within 0.5 of group 
> "Protein"' -ofpdb
>
>
> Nothing comes up when I enter them. Please could someone help me with this?
>
>
> Akash
> --
> 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.
>
--
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.
-- 
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.

Re: [gmx-users] gmx select

[Mark Abraham]

Hi,

What are the residue names in your coordinate file? Glyci probably doesn't
fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
wrote:

> Hi all,
>
>
> I am trying to select all the glycine molecules with 0.5nm of my protein.
> I tried both of these commands I got from the gromacs website:
>
> gmx select -f output.gro -select "Close to protein" resname Glyci and
> within 0.5 of group "Protein"' -ofpdb
>
> gmx select -f output.xtc -s output.tpr (my converted input file) -select
> "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb
>
>
> Nothing comes up when I enter them. Please could someone help me with this?
>
>
> Akash
> --
> 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.
>
-- 
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.

[gmx-users] gmx select

[Pandya, Akash]

Hi all,


I am trying to select all the glycine molecules with 0.5nm of my protein. I 
tried both of these commands I got from the gromacs website:

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"' -ofpdb

gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close 
to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb


Nothing comes up when I enter them. Please could someone help me with this?


Akash
-- 
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.

[gmx-users] Non-periodic COM Pulling

[Daniel Kozuch]

Hello,

Is it possible to do non-periodic COM pulling using the distance function
in GMX 5.14 (i.e. where the distance between the two groups is calculated
ignoring pbc)?

In the tutorials/online the solution seems to be to simply use a box twice
the size of the largest pulling distance, but that would be very
computationally expensive for me.

Best,
Dan
-- 
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.

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

[Mark Abraham]

Hi,

Sure. But who has data that shows that e.g. a free-energy calculation with
the defaults produces lower quality observables than you get with the
defaults?

Mark

On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane <
stephane.teletc...@univ-nantes.fr> wrote:

> Le 11/07/2017 à 15:24, Mark Abraham a écrit :
> > Guessing wildly, the cost of your simulation is probably at least double
> > what the defaults would give, and for that cost, I'd want to know why.
>
> Estimated colleague,
>
> Since this is a wild guess, I'd think to add some guesses myself. I
> remember "some time" back having used a lower tolerance on Ewald for
> amber simulations (around amber 4/5/6 ...) and it was more common at
> this time I presume. This may also be linked to the fact that amber has
> a short cut-off at 8 angstrom for electrostatics ...
> Someone apparently "ill" at the time already found this stane in 2009:
>
>
> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber
>
> Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER,
> and this is mentioned here:
>
> http://ambermd.org/Questions/ewald.html
>
> ... apparently linked to DNA simulation as found in JACS 117,4193 (1995)
>
> In short, this value may come in back and forth for "historical" reasons
> (and misuse, of course).
>
> Others may have additional comments :-)
>
> Best,
>
> Stéphane
>
>
> --
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
> --
> 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.
-- 
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.

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

You need to have a file that contains the frame you want to start from, and
give that to gmx grompp -t

Mark

On Wed, Jul 12, 2017 at 5:54 PM CLARK NICOLAS Joan 
wrote:

> Dear gmx users,
>
>
> I am trying to extend a finished simulation from a frame which is not the
> last one in my trajectory. I have tried convert-tpr but I think it's only
> modifying the number of steps because the resulting tpr file starts the
> simulation from the first or the last frame depending on whether or not I
> supply the cpt file to mdrun.
>
>
> Is there any way to do what I am trying or is using grompp every time my
> only choice?
>
>
> Thanks,
>
> Joan
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> --
> 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.
-- 
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.

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

[Téletchéa Stéphane]

Le 11/07/2017 à 15:24, Mark Abraham a écrit :

Guessing wildly, the cost of your simulation is probably at least double
what the defaults would give, and for that cost, I'd want to know why.


Estimated colleague,

Since this is a wild guess, I'd think to add some guesses myself. I 
remember "some time" back having used a lower tolerance on Ewald for 
amber simulations (around amber 4/5/6 ...) and it was more common at 
this time I presume. This may also be linked to the fact that amber has 
a short cut-off at 8 angstrom for electrostatics ...

Someone apparently "ill" at the time already found this stane in 2009:

http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber

Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER, 
and this is mentioned here:


http://ambermd.org/Questions/ewald.html

... apparently linked to DNA simulation as found in JACS 117,4193 (1995)

In short, this value may come in back and forth for "historical" reasons 
(and misuse, of course).


Others may have additional comments :-)

Best,

Stéphane


--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 
Nantes cedex 03, France

Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
--
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.

[gmx-users] (no subject)

[CLARK NICOLAS Joan]

Dear gmx users,


I am trying to extend a finished simulation from a frame which is not the last 
one in my trajectory. I have tried convert-tpr but I think it's only modifying 
the number of steps because the resulting tpr file starts the simulation from 
the first or the last frame depending on whether or not I supply the cpt file 
to mdrun.


Is there any way to do what I am trying or is using grompp every time my only 
choice?


Thanks,

Joan
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
-- 
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.

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

[Jose Borreguero]

will do, thanks for the tip.

On Wed, Jul 12, 2017 at 11:42 AM, Mark Abraham 
wrote:

> Hi,
>
> That kind of information is in the release notes, e.g. at
> http://manual.gromacs.org/documentation/. Perhaps you want to start with
> the 2016 ones :-)
>
> Mark
>
> On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero 
> wrote:
>
> > Dear Gromacs users,
> >
> > I'm a relatively new user of Gromacs and recently realized there is a
> > "2016" branch that is still being updated. What is the difference with
> the
> > 5.x branch?
> >
> > I ask because I could find RPM packages only for the 2016 version, much
> > easier to install than building from source.
> >
> > Best,
> > .Jose
> > --
> > 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.
> >
> --
> 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.
>
-- 
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.

Re: [gmx-users] RDF

[Saikat Pal]

Dear Vidya.R
Its very difficult to answer this question.It depends on your system .If you 
run more time of your system, RDF will be more smooth

Saikat Pal
IIT GUWAHATI



On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya R  
wrote:

Hi,

I want to calculate RDF of my organic molecule with a solvent.

What should be the duration of my simulation?

Is 100 ps enough?


Thanks,
Vidya.R
-- 
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.
-- 
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.

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

[Mark Abraham]

Hi,

That kind of information is in the release notes, e.g. at
http://manual.gromacs.org/documentation/. Perhaps you want to start with
the 2016 ones :-)

Mark

On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero 
wrote:

> Dear Gromacs users,
>
> I'm a relatively new user of Gromacs and recently realized there is a
> "2016" branch that is still being updated. What is the difference with the
> 5.x branch?
>
> I ask because I could find RPM packages only for the 2016 version, much
> easier to install than building from source.
>
> Best,
> .Jose
> --
> 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.
>
-- 
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.

[gmx-users] what is the difference between the 2016.x and the 5.x series?

[Jose Borreguero]

Dear Gromacs users,

I'm a relatively new user of Gromacs and recently realized there is a
"2016" branch that is still being updated. What is the difference with the
5.x branch?

I ask because I could find RPM packages only for the 2016 version, much
easier to install than building from source.

Best,
.Jose
-- 
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.

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

I would avoid using the combination of position restraints and constrained
bonds with an input structure that is not necessarily consistent with the
constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that my
starting structure was special *and* saw a large deformation if I didn't
use the restraints. If I saw the deformation, I would wonder why I thought
it was special.

If you're trying to relax a thing, let it relax. :-) If something strange
happens, consider that when it has happened. Obviously that means you want
to look at what happens when you did your equilibration, but you were going
to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  wrote:

> hi,
>
> I've seen with vmd the gro file generated after the transformation, and
> after the 2 steps of minimization,
> it seems that they have no problem,
> while if I see the step_n.pdb file generated before the crash, there are
> some atoms far away from the rest of the protein, while this is not
> happening if I comment the restrains part
>
>
> do you understand why??
>
> thank you again,
> Emiliano
>
>
>
> On 2017-07-12 16:29, Mark Abraham wrote:
> > Hi,
> >
> > Those are all good things, but have you actually got out a molecular
> > viewer
> > and looked at the input and output of your resolution conversion?
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> > wrote:
> >
> >> Hi,
> >> thanks for the prompt answer,
> >>
> >>
> >> I've found the same problem even if I try to convert the coarse
> >> grained
> >> pdb obtained from martinize.py, so in that case it should be not a
> >> problem to have the conversion, for this reason I though it is a
> >> methodological problem...
> >>
> >> I've seen the blowing-up issues , but I think:
> >> - the timestep is enough small  (0.0002)
> >> -the system should be enough minimized via the previous steps (in fact
> >> the sd converged to the machine precision in both cases, actually the
> >> potential energy is ~10^5, but I don't know how to reduce it, I tried
> >> a
> >> cg after the sd, but the proble is still there)
> >> -there in not any pressure coupling
> >> -I've tried a different temperature coupling (berensden, nose-hoover)
> >> and it doesn't work
> >> - the md stops at the first step, so there is not any .edr file
> >> produced
> >> to be looked at
> >>
> >>
> >>
> >> I don't know what else to do...
> >>
> >> maybe, do you know another conversion protocol to use??
> >>
> >>
> >> thank you again
> >> Emiliano
> >>
> >> On 2017-07-12 15:11, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > Sounds like you might be
> >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
> the
> >> > conversion doesn't work for your configuration. You should start by
> >> > doing a
> >> > visual check of the configuration for sanity, then follow the advice
> in
> >> > that link.
> >> >
> >> > Mark
> >> >
> >> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> >> > wrote:
> >> >
> >> >> dear all,
> >> >>
> >> >> I am facing a problem with the conversion from Martini CG
> >> >> representation
> >> >> to All-atomistic one.
> >> >>
> >> >> I am using the initram.sh wrapper around the backward.py.
> >> >>
> >> >> There is a LINCS warning problem when the energy relaxation is
> >> >> performed
> >> >> using position restrained md
> >> >> (I've also tried to run grompp and mdrun commands directly from the
> >> >> terminal and the error persists, so it is not a wrapper problem).
> >> >>
> >> >> this is the .mdp file generated by the script:
> >> >>
> >> >> "define   = -DPOSRES
> >> >> integrator   = md
> >> >> nsteps   = 500
> >> >> dt   = 0.0002
> >> >> pbc  = xyz
> >> >>
> >> >> rcoulomb = 0.9
> >> >> rlist= 0.9
> >> >> rvdw = 0.9
> >> >>
> >> >> tcoupl   = v-rescale
> >> >> ref_t= 200
> >> >> tau_t= 0.1
> >> >> tc_grps  = System
> >> >>
> >> >> gen_vel  = yes
> >> >> gen_temp = 300
> >> >>
> >> >> constraints  = all-bonds "
> >> >>
> >> >>
> >> >> this is the error I found in the .log file:
> >> >>
> >> >> "Fatal error:
> >> >> Too many LINCS warnings (1034)
> >> >> If you know what you are doing you can adjust the lincs warning
> >> >> threshold in your mdp file
> >> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> >> but normally it is better to fix the problem "
> >> >>
> >> >> I tired to comment the constrains part and all is working, but since
> >> >> the
> >> >> structure should not be altered too much, I think the constraints are
> >> >> required (if I constrain only the h-bonds, it is also working).
> >> >>
> >> >> I've also added to the .mdp 

Re: [gmx-users] LINCS warning during constrained md

[edesantis]

hi,

I've seen with vmd the gro file generated after the transformation, and 
after the 2 steps of minimization,

it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there are 
some atoms far away from the rest of the protein, while this is not 
happening if I comment the restrains part



do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:

Hi,

Those are all good things, but have you actually got out a molecular 
viewer

and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  
wrote:



Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse 
grained

pdb obtained from martinize.py, so in that case it should be not a
problem to have the conversion, for this reason I though it is a
methodological problem...

I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact
the sd converged to the machine precision in both cases, actually the
potential energy is ~10^5, but I don't know how to reduce it, I tried 
a

cg after the sd, but the proble is still there)
-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover)
and it doesn't work
- the md stops at the first step, so there is not any .edr file 
produced

to be looked at



I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:
> Hi,
>
> Sounds like you might be
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> conversion doesn't work for your configuration. You should start by
> doing a
> visual check of the configuration for sanity, then follow the advice in
> that link.
>
> Mark
>
> On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> wrote:
>
>> dear all,
>>
>> I am facing a problem with the conversion from Martini CG
>> representation
>> to All-atomistic one.
>>
>> I am using the initram.sh wrapper around the backward.py.
>>
>> There is a LINCS warning problem when the energy relaxation is
>> performed
>> using position restrained md
>> (I've also tried to run grompp and mdrun commands directly from the
>> terminal and the error persists, so it is not a wrapper problem).
>>
>> this is the .mdp file generated by the script:
>>
>> "define   = -DPOSRES
>> integrator   = md
>> nsteps   = 500
>> dt   = 0.0002
>> pbc  = xyz
>>
>> rcoulomb = 0.9
>> rlist= 0.9
>> rvdw = 0.9
>>
>> tcoupl   = v-rescale
>> ref_t= 200
>> tau_t= 0.1
>> tc_grps  = System
>>
>> gen_vel  = yes
>> gen_temp = 300
>>
>> constraints  = all-bonds "
>>
>>
>> this is the error I found in the .log file:
>>
>> "Fatal error:
>> Too many LINCS warnings (1034)
>> If you know what you are doing you can adjust the lincs warning
>> threshold in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem "
>>
>> I tired to comment the constrains part and all is working, but since
>> the
>> structure should not be altered too much, I think the constraints are
>> required (if I constrain only the h-bonds, it is also working).
>>
>> I've also added to the .mdp file the lines:
>> " lincs-order  = 4 (or 2 or 8)
>> lincs-iter   = 1 (or 2 or 10)
>> "
>> but it is still not working...
>>
>>
>> any of you have suggestions to solve the problem??
>> how is it possible to change the environment variable?
>>
>>
>> thanks in advance for your help
>> Emiliano
>>
>> --
>> Emiliano De Santis
>>
>> --
>> 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.
>>

--
Emiliano De Santis
--
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.



--
Emiliano De Santis
--
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

* 

[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components

[Nuria Codina]

Hi,

I want to measure the Hydrophobic and Hydrophilic components of the Solvent
Accessible Surface Area. In the Tool Changes for 5.0 I found these command:

gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output
'"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B"
and not charge {-0.2 to 0.2}; "Total" group "B"'

And I tried changing "A" and "B" for "protein", but it is not working for
me. Could you show me an specific example that worked for you?

Thanks very much,
Núria
-- 
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.

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Those are all good things, but have you actually got out a molecular viewer
and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  wrote:

> Hi,
> thanks for the prompt answer,
>
>
> I've found the same problem even if I try to convert the coarse grained
> pdb obtained from martinize.py, so in that case it should be not a
> problem to have the conversion, for this reason I though it is a
> methodological problem...
>
> I've seen the blowing-up issues , but I think:
> - the timestep is enough small  (0.0002)
> -the system should be enough minimized via the previous steps (in fact
> the sd converged to the machine precision in both cases, actually the
> potential energy is ~10^5, but I don't know how to reduce it, I tried a
> cg after the sd, but the proble is still there)
> -there in not any pressure coupling
> -I've tried a different temperature coupling (berensden, nose-hoover)
> and it doesn't work
> - the md stops at the first step, so there is not any .edr file produced
> to be looked at
>
>
>
> I don't know what else to do...
>
> maybe, do you know another conversion protocol to use??
>
>
> thank you again
> Emiliano
>
> On 2017-07-12 15:11, Mark Abraham wrote:
> > Hi,
> >
> > Sounds like you might be
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> > conversion doesn't work for your configuration. You should start by
> > doing a
> > visual check of the configuration for sanity, then follow the advice in
> > that link.
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> > wrote:
> >
> >> dear all,
> >>
> >> I am facing a problem with the conversion from Martini CG
> >> representation
> >> to All-atomistic one.
> >>
> >> I am using the initram.sh wrapper around the backward.py.
> >>
> >> There is a LINCS warning problem when the energy relaxation is
> >> performed
> >> using position restrained md
> >> (I've also tried to run grompp and mdrun commands directly from the
> >> terminal and the error persists, so it is not a wrapper problem).
> >>
> >> this is the .mdp file generated by the script:
> >>
> >> "define   = -DPOSRES
> >> integrator   = md
> >> nsteps   = 500
> >> dt   = 0.0002
> >> pbc  = xyz
> >>
> >> rcoulomb = 0.9
> >> rlist= 0.9
> >> rvdw = 0.9
> >>
> >> tcoupl   = v-rescale
> >> ref_t= 200
> >> tau_t= 0.1
> >> tc_grps  = System
> >>
> >> gen_vel  = yes
> >> gen_temp = 300
> >>
> >> constraints  = all-bonds "
> >>
> >>
> >> this is the error I found in the .log file:
> >>
> >> "Fatal error:
> >> Too many LINCS warnings (1034)
> >> If you know what you are doing you can adjust the lincs warning
> >> threshold in your mdp file
> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> but normally it is better to fix the problem "
> >>
> >> I tired to comment the constrains part and all is working, but since
> >> the
> >> structure should not be altered too much, I think the constraints are
> >> required (if I constrain only the h-bonds, it is also working).
> >>
> >> I've also added to the .mdp file the lines:
> >> " lincs-order  = 4 (or 2 or 8)
> >> lincs-iter   = 1 (or 2 or 10)
> >> "
> >> but it is still not working...
> >>
> >>
> >> any of you have suggestions to solve the problem??
> >> how is it possible to change the environment variable?
> >>
> >>
> >> thanks in advance for your help
> >> Emiliano
> >>
> >> --
> >> Emiliano De Santis
> >>
> >> --
> >> 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.
> >>
>
> --
> Emiliano De Santis
> --
> 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.
>
-- 
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.

Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse grained 
pdb obtained from martinize.py, so in that case it should be not a 
problem to have the conversion, for this reason I though it is a 
methodological problem...


I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact 
the sd converged to the machine precision in both cases, actually the 
potential energy is ~10^5, but I don't know how to reduce it, I tried a 
cg after the sd, but the proble is still there)

-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover) 
and it doesn't work
- the md stops at the first step, so there is not any .edr file produced 
to be looked at




I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by 
doing a

visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  
wrote:



dear all,

I am facing a problem with the conversion from Martini CG 
representation

to All-atomistic one.

I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is 
performed

using position restrained md
(I've also tried to run grompp and mdrun commands directly from the
terminal and the error persists, so it is not a wrapper problem).

this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since 
the

structure should not be altered too much, I think the constraints are
required (if I constrain only the h-bonds, it is also working).

I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
Emiliano De Santis

--
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.



--
Emiliano De Santis
--
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.

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by doing a
visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  wrote:

> dear all,
>
> I am facing a problem with the conversion from Martini CG representation
> to All-atomistic one.
>
> I am using the initram.sh wrapper around the backward.py.
>
> There is a LINCS warning problem when the energy relaxation is performed
> using position restrained md
> (I've also tried to run grompp and mdrun commands directly from the
> terminal and the error persists, so it is not a wrapper problem).
>
> this is the .mdp file generated by the script:
>
> "define   = -DPOSRES
> integrator   = md
> nsteps   = 500
> dt   = 0.0002
> pbc  = xyz
>
> rcoulomb = 0.9
> rlist= 0.9
> rvdw = 0.9
>
> tcoupl   = v-rescale
> ref_t= 200
> tau_t= 0.1
> tc_grps  = System
>
> gen_vel  = yes
> gen_temp = 300
>
> constraints  = all-bonds "
>
>
> this is the error I found in the .log file:
>
> "Fatal error:
> Too many LINCS warnings (1034)
> If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem "
>
> I tired to comment the constrains part and all is working, but since the
> structure should not be altered too much, I think the constraints are
> required (if I constrain only the h-bonds, it is also working).
>
> I've also added to the .mdp file the lines:
> " lincs-order  = 4 (or 2 or 8)
> lincs-iter   = 1 (or 2 or 10)
> "
> but it is still not working...
>
>
> any of you have suggestions to solve the problem??
> how is it possible to change the environment variable?
>
>
> thanks in advance for your help
> Emiliano
>
> --
> Emiliano De Santis
>
> --
> 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.
>
-- 
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.

[gmx-users] Walls and PME for long range electrostatics

[Alexander Miessen]

Dear all,


I am simulating a Au(111) slab with explicit electrons inside (included 
as a "free electron gas"). The gold atoms are frozen, the electrons are 
free but confined inside the slab by a more repulsive pair interaction 
with the Au-surface atoms. This works fine and simulations are stable.


I am using a xy-periodicity. For this I introduced walls on both sides 
of the box. My wall-atoms dont interact with any of my atoms.


For a couple weeks now, I have been trying to reproduce image charge 
effects with this model, freezing a test charge (no LJ-interaction, only 
a charge of +1e assigned to it) at a certain distance from the Au 
surface. In the documentation it is stated that z_box should be 3 times 
as big as the system when using walls with a slab geometry. I did this. 
But the forces I calculate on the test charge neither match for the far 
field, nor for the near field.


Do you have any suggestions on how the walls and therefore PME might 
bring artifacts in? I am running out of ideas on how to fix this problem.



Thanks,

Alex
--
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.

[gmx-users] LINCS warning during constrained md

[edesantis]

dear all,

I am facing a problem with the conversion from Martini CG representation 
to All-atomistic one.


I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is performed 
using position restrained md
(I've also tried to run grompp and mdrun commands directly from the 
terminal and the error persists, so it is not a wrapper problem).


this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since the 
structure should not be altered too much, I think the constraints are 
required (if I constrain only the h-bonds, it is also working).


I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
Emiliano De Santis

--
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.

Re: [gmx-users] ACETONITRILE with CHARM ff

[Sonia Milena Aguilera Segura]

> 
> Message: 3
> Date: Tue, 11 Jul 2017 12:57:05 -0400
> From: Justin Lemkul 
> > Moreover, I observed that this time I got lower values for P during the NPT
> > equilibration, but still is too far from 1 bar.  I really don't understand
> > why for the NVT simulation I get a T around 298, but as soon as I turn on
> > the pcoupl, the T rises to 300-301 K and the P gets average values of 7
> > and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of
> > the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7
> > bar. Considering the parameters I am using, is there anything I can change
> > to make the P coupling better? I am running a 3 nm box with 308 molecules.
> > This is the full mdp file:
> > 
> 
> http://www.gromacs.org/Documentation/Terminology/Pressure
> 
> Your box is very small and will be subject to large fluctuations.

Dear Justin, 

I increased the size of the simulation box to 4 nm. Indeed, the values of 
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T 
keeps being overestimated (302 K). During NVT I got the right value, so I 
decided to run the 200 ns NPT equilibration with Berendsen barostat instead of 
P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. 
Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the 
-e option because it gives me the error Could not find energy term named 
'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect 
stored values for it?. But I am using -t ). Despite I got low pressure averages 
around 0.5 bar, the temperature raised again to 301-302. This happens very 
early in the simulation, which seems to indicate that for sd 
integrator/thermostat and P-R barostat there is something going on. I am 
getting practically the same density in between simulation, so I guess I can 
say tha
 t in term of P, the system has been equilibrated. However, what can I do to 
get the right T for this system? If I was able to get the right T with 
Berendsen barostat, I don't understand what's wrong when I change to P-R. 

Thank you in advance, 

Sonia Aguilera 
PhD student
ENSCM

> 
> -Justin
> 
> > ; Run control
> > integrator   = sd   ; Langevin dynamics
> > tinit= 0
> > dt   = 0.0005
> > nsteps   = 200   ; 1 ns
> > nstcomm  = 100
> > ;energygrps  = non-Water
> > ; Neighborsearching and short-range nonbonded interactions
> > cutoff-scheme= verlet
> > nstlist  = 20
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.2
> > ; Electrostatics
> > coulombtype  = PME
> > rcoulomb = 1.2
> > ; van der Waals
> > vdwtype  = cutoff
> > vdw-modifier = force-switch
> > rvdw-switch  = 1.0
> > rvdw = 1.2
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr  = no
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing   = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme_order= 6
> > ewald_rtol   = 1e-06
> > epsilon_surface  = 0
> > ; Temperature coupling
> > ; tcoupl is implicitly handled by the sd integrator
> > tc_grps  = system
> > tau_t= 1.0
> > ref_t= 298.15
> > ; Pressure coupling is on for NPT
> > Pcoupl   = Parrinello-Rahman
> > tau_p= 1.0
> > compressibility  = 4.5e-05
> > ref_p= 1.0
> > ; Do not generate velocities
> > gen_vel  = no
> > ; options for bonds
> > constraints  = none  ; we only have C-H bonds here
> > ; Type of constraint algorithm
> > constraint-algorithm = lincs
> > ; Constrain the starting configuration
> > ; since we are continuing from NPT
> > continuation = yes
> > ; Highest order in the expansion of the constraint coupling matrix
> > lincs-order  = 12
> > 
> > 
> > Thank you very much,
> > 
> > Sonia Aguilera
> > PhD student
> > ENSCM
> >> ; Run control
> >> integrator   = sd   ; Langevin dynamics
> >> tinit= 0
> >> dt   = 0.0005
> >> nsteps   = 4000   ; 20 ns
> >> nstcomm  = 100
> >> ; Neighborsearching and short-range nonbonded interactions
> >> cutoff-scheme= verlet
> >> nstlist  = 20
> >> ns_type  = grid
> >> pbc  = xyz
> >> rlist= 1.2
> >> ; Electrostatics
> >> coulombtype  = PME
> >> rcoulomb = 1.2
> >> ; van der Waals
> >> vdwtype  = cutoff
> >> vdw-modifier = potential-switch
> >> rvdw-switch  = 1.0
> >> rvdw = 1.2
> >> ; 

Re: [gmx-users] output pdb reformatted

[Mark Abraham]

Hi,

Please stop doing that. You're risking wasting your own time as well. ;-)

Mark

On Tue, Jul 11, 2017 at 11:52 PM Alex  wrote:

> You are absolutely right once again. I've been glancing over that topology,
> looking right at what the problem was, and not seeing it. The residue name
> column was empty, all atom types went to crap, but because I always grompp
> with -maxwarn 10 (for completely unrelated warnings in completely different
> simulations) everything seemed okay.
>
> Thanks!
>
> Alex
>
> On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/11/17 4:01 PM, Alex wrote:
> >
> >> Hi all,
> >>
> >> I have a tiny acetonitrile molecule here. The input pdb prior to EM is
> >> this:
> >>
> >> TITLE Gromacs Runs On Most of All Computer Systems
> >> REMARKTHIS IS A SIMULATION BOX
> >> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
> >> MODEL1
> >> ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
> >>C
> >> ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
> >>H
> >> ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
> >>H
> >> ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
> >>H
> >> ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
> >>C
> >> ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
> >>N
> >> TER
> >> ENDMDL
> >>
> >> The output, however, is this:
> >>
> >> TITLE Great Red Owns Many ACres of Sand
> >> REMARKTHIS IS A SIMULATION BOX
> >> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
> >> MODEL1
> >> ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
> >>C
> >> ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
> >>H
> >> ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
> >>H
> >> ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
> >>H
> >> ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
> >>C
> >> ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
> >>N
> >> TER
> >> ENDMDL
> >>
> >> Why? I don't think I've seen this happen before, and I'd like to keep
> the
> >> initial format. Any suggestions? My itp is for an ACT residue, which is
> >> included in the simulation topology input.
> >>
> >>
> > mdrun gets the residue and atom names from the topology, so a dump of the
> > .tpr should show something useful.  It seems like something in the
> topology
> > has gotten broken - atom names becoming numbers, residue name becoming
> the
> > atom names.  Bizarre.  grompp should have complained loudly if there were
> > mismatches between coordinates and topology.
> >
> > -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
> >
> > * 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.
> >
> --
> 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.
>
-- 
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.

[gmx-users] topology servers versus ff

[ABEL Stephane]

Hello,

If you want to use CHARMM for your simulations, do not use PRODRUG to construct 
your parameters but use ParamChem, instead. 

https://www.paramchem.org/

Stéphane

--

Message: 2
Date: Wed, 12 Jul 2017 14:36:27 +0500
From: maria khan 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] topology servers versus ff.
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Dear gromacs users..

while using charmm27 can i use PRODRUG for topology building.??

when im using prodrug pdb2gmx gives me error of missing atoms but when i
use charmm ff,it doesnt give me that error,so proceeding with charmm27 i
made ligand topology by prodrug and used it for further simulation,when
comes to adding ions step it gives me error of ""atomtypes CH3 not found"".

thanks.


--

--
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.

End of gromacs.org_gmx-users Digest, Vol 159, Issue 58
**
-- 
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.

[gmx-users] topology servers versus ff.

[maria khan]

Dear gromacs users..

while using charmm27 can i use PRODRUG for topology building.??

when im using prodrug pdb2gmx gives me error of missing atoms but when i
use charmm ff,it doesnt give me that error,so proceeding with charmm27 i
made ligand topology by prodrug and used it for further simulation,when
comes to adding ions step it gives me error of ""atomtypes CH3 not found"".

thanks.
-- 
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.

[gmx-users] Benchmarks v5.0

[jony.castagna]

Hi there,
  where can I find the benchmark input files for the 2 cases reported in this 
paper (ion channel and ethanol-water system)?

http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf

Many thanks.
Jony

Dr Jony Castagna
Sci-Tech Daresbury
Keckwick Lane
Daresbury
Warrington
WA4 4AD
Tel.: +44 (0)1925 603682

-- 
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.

Re: [gmx-users] Add missing residues

[Nikhil Maroli]

http://www.charmm-gui.org/

-- 
Regards,
Nikhil Maroli
-- 
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.

[gmx-users] Add missing residues

[Khadija Amine]

Hello everyone,
Can someone post the best tool available for building missing residues in
the crystal structure?
I need the complete structure (2 missing residues) for carrying out
simulation studies.
 Thank you

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
-- 
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.