[gmx-users] gmx rdf gromacs 5.1 question!

[Stelios Karozis]

Greeting everyone,
I strated using gromacs 5.1 and I have difficulties with gmx rdf
command. With older version of gromacs I used -xy -rdf mol_com
 flags. As far as I can understand, the equivalent flags for gromacs 5.1
 are -xy -selrpos mol_com but the result is not correct. For instance
 the first peak is at 0nm and not close to 0.5nm...
I believe I am not using the right flags. 

Thanks in advance for your help

-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 
-- 
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 rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

You should use -seltype instead of -selrpos in this case.

Best regards,
Teemu

On Fri, Sep 25, 2015, 11:12 Stelios Karozis 
wrote:

> Greeting everyone,
> I strated using gromacs 5.1 and I have difficulties with gmx rdf
> command. With older version of gromacs I used -xy -rdf mol_com
>  flags. As far as I can understand, the equivalent flags for gromacs 5.1
>  are -xy -selrpos mol_com but the result is not correct. For instance
>  the first peak is at 0nm and not close to 0.5nm...
> I believe I am not using the right flags.
>
> Thanks in advance for your help
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
> --
> 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] gromacs 5.0.5 install

[신은혜]

I installed gromacs 5.0.5, but during installation, i got error massages
 
CMake Error at src/programs/cmake_install.cmake:42 (FILE):
  file INSTALL cannot find
  "//phome01/p580seh/gromacs-5.0.5/build/bin/gmx_mpi_d".
Call Stack (most recent call first):
  src/cmake_install.cmake:40 (INCLUDE)
  cmake_install.cmake:48 (INCLUDE)

make: *** [install] Error 1 
 
I also check this option : -DGMX_MPI=on
 
how to fix it ?
 
-- 
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 rdf gromacs 5.1 question!

[Stelios Karozis]

Hi Teemu
Thanks for your response, but -seltype is not available as a flag for
gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
it a try...)

-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 


On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
 wrote :

> Hi,
> 
> You should use -seltype instead of -selrpos in this case.
> 
> Best regards,
> Teemu
> 
> On Fri, Sep 25, 2015, 11:12 Stelios Karozis
>  wrote:
> 
> > Greeting everyone,
> > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > command. With older version of gromacs I used -xy -rdf mol_com
> >  flags. As far as I can understand, the equivalent flags for
> > gromacs 5.1 are -xy -selrpos mol_com but the result is not correct.
> > For instance the first peak is at 0nm and not close to 0.5nm...
> > I believe I am not using the right flags.
> >
> > Thanks in advance for your help
> >
> > --
> > Karozis Stelios
> > Chemical Engineer, MSc
> > Research Associate at EREL
> > NCSR D- INRASTES
> > tel:0030 210 650 3403
> > e-mail: skaro...@ipta.demokritos.gr
> > --
> > 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 rdf gromacs 5.1 question!

[Teemu Murtola]

Hi,

indeed, this appears to be a bug, likely originating already from 5.0
times. I'll try to fix that soon. But it is just a convenience option,
anyways: you can always write each of your selections as "mol_com of ...",
and it should work the same.

Best regards,
Teemu

On Fri, Sep 25, 2015 at 11:50 AM Stelios Karozis <
skaro...@ipta.demokritos.gr> wrote:

> Hi Teemu
> Thanks for your response, but -seltype is not available as a flag for
> gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
> it a try...)
>
> --
> Karozis Stelios
> Chemical Engineer, MSc
> Research Associate at EREL
> NCSR D- INRASTES
> tel:0030 210 650 3403
> e-mail: skaro...@ipta.demokritos.gr
>
>
> On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
>  wrote :
>
> > Hi,
> >
> > You should use -seltype instead of -selrpos in this case.
> >
> > Best regards,
> > Teemu
> >
> > On Fri, Sep 25, 2015, 11:12 Stelios Karozis
> >  wrote:
> >
> > > Greeting everyone,
> > > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > > command. With older version of gromacs I used -xy -rdf mol_com
> > >  flags. As far as I can understand, the equivalent flags for
> > > gromacs 5.1 are -xy -selrpos mol_com but the result is not correct.
> > > For instance the first peak is at 0nm and not close to 0.5nm...
> > > I believe I am not using the right flags.
> > >
> > > Thanks in advance for your help
> > >
> > > --
> > > Karozis Stelios
> > > Chemical Engineer, MSc
> > > Research Associate at EREL
> > > NCSR D- INRASTES
> > > tel:0030 210 650 3403
> > > e-mail: skaro...@ipta.demokritos.gr
> > > --
> > > 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 rdf gromacs 5.1 question!

[Stelios Karozis]

Thanks with selections syntax it works!


-- 
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr 


On Fri, 25 Sep 2015 12:05:41 +0300, "Teemu Murtola"
 wrote :

> Hi,
> 
> indeed, this appears to be a bug, likely originating already from 5.0
> times. I'll try to fix that soon. But it is just a convenience option,
> anyways: you can always write each of your selections as "mol_com
> of ...", and it should work the same.
> 
> Best regards,
> Teemu
> 
> On Fri, Sep 25, 2015 at 11:50 AM Stelios Karozis <
> skaro...@ipta.demokritos.gr> wrote:
> 
> > Hi Teemu
> > Thanks for your response, but -seltype is not available as a flag
> > for gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd
> > (I gave it a try...)
> >
> > --
> > Karozis Stelios
> > Chemical Engineer, MSc
> > Research Associate at EREL
> > NCSR D- INRASTES
> > tel:0030 210 650 3403
> > e-mail: skaro...@ipta.demokritos.gr
> >
> >
> > On Fri, 25 Sep 2015 11:23:39 +0300, "Teemu Murtola"
> >  wrote :
> >
> > > Hi,
> > >
> > > You should use -seltype instead of -selrpos in this case.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Fri, Sep 25, 2015, 11:12 Stelios Karozis
> > >  wrote:
> > >
> > > > Greeting everyone,
> > > > I strated using gromacs 5.1 and I have difficulties with gmx rdf
> > > > command. With older version of gromacs I used -xy -rdf mol_com
> > > >  flags. As far as I can understand, the equivalent flags for
> > > > gromacs 5.1 are -xy -selrpos mol_com but the result is not
> > > > correct. For instance the first peak is at 0nm and not close to
> > > > 0.5nm... I believe I am not using the right flags.
> > > >
> > > > Thanks in advance for your help
> > > >
> > > > --
> > > > Karozis Stelios
> > > > Chemical Engineer, MSc
> > > > Research Associate at EREL
> > > > NCSR D- INRASTES
> > > > tel:0030 210 650 3403
> > > > e-mail: skaro...@ipta.demokritos.gr
> > > > --
> > > > 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.
 
-- 
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] PTR is not found in residue topology database

[Amali Guruge]

Dear all,

My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA.
When I run the command pdb2gmx, it gives an error stating that PTR is not
found in residue topology database.

How can I fix this problem?
Can anyone help me?

Thank you.
-- 
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] PTR is not found in residue topology database

[Justin Lemkul]

On 9/25/15 10:50 AM, Amali Guruge wrote:

Dear all,

My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA.
When I run the command pdb2gmx, it gives an error stating that PTR is not
found in residue topology database.

How can I fix this problem?
Can anyone help me?



http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-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.

Re: [gmx-users] gromacs 5.0.5 install

[Mark Abraham]

Hi,

That kind of error usually means you're trying to install into the build
tree, or something like that. Source, build and install locations should be
different.

Mark

On Fri, Sep 25, 2015 at 10:42 AM 신은혜  wrote:

> I installed gromacs 5.0.5, but during installation, i got error massages
>
> CMake Error at src/programs/cmake_install.cmake:42 (FILE):
>   file INSTALL cannot find
>   "//phome01/p580seh/gromacs-5.0.5/build/bin/gmx_mpi_d".
> Call Stack (most recent call first):
>   src/cmake_install.cmake:40 (INCLUDE)
>   cmake_install.cmake:48 (INCLUDE)
>
> make: *** [install] Error 1
>
> I also check this option : -DGMX_MPI=on
>
> how to fix it ?
>
> --
> 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] Optimize the cut-off distance and fourierspacing

[Mark Abraham]

Hi,

mdrun uses -tunepme by default, which does this. You can learn more about
the theory behind the implementation in the PDF reference manual. There is
also gmx tune_pme to scan a larger range of parameters than mdrun can.

Mark

On Fri, Sep 25, 2015 at 4:12 AM Vy Phan  wrote:

> Dear All gromacs Users,
>
> Could you please tell me the way to optimize the cut-off distance and
> fourierspacing on Gromacs 5.0.4 ?
>
> Thank you so much
> Phan Vy
> --
> 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] Prospective research areas of GROMACS

[Sabyasachi Sahoo]

Thanks a lot for such in-depth insight! Will look into all of this and get
started asap!

On Wed, Sep 23, 2015 at 1:29 AM, Mark Abraham 
wrote:

> Hi,
>
> On Mon, Sep 21, 2015 at 7:10 PM Sabyasachi Sahoo 
> wrote:
>
> > Dear Gromacs users and developers,
> >
> > I am a parallel programming researcher and would like to contribute to
> > Gromacs molecular dynamics software by helping to nail down any
> bottlenecks
> > that occur in scaling of the software on multiple CPUs (and probably
> > improved performance in exa-scale era.) I am already in process of
> > collecting profiling results to identify the phases that can be improved
> > (and also for few other MD softwares).
> >
>
> Welcome! (And good luck... optimizing software that's had over 10 years of
> performance focussed effort is... challenging!)
>
> Profiling is itself problematic. Assuming one can get GROMACS to build with
> whatever constraints the tool adds, and can benchmark on a machine where
> you do not suffer contention for network resources, one needs to produce
> more useful information than can already be obtained at the end of the .log
> file. Such data is most interesting only when near the strong scaling limit
> (e.g. < 100 particles per CPU core) and thus at very short per-MD-step
> times (several wallclock milliseconds). Neither function instrumentation,
> nor sampling tend to work well in this regime. But we'd love to be
> surprised :-)
>
> Hence, I would request all of you to please suggest me some possible areas
> > of research, on which we can work on, for better scaling of Gromacs,
> > (and/or MD softwares in general.) Going through the official website
> > documentation helps me realise that implementing a truly parallel FFT (or
> > making it scale better) in Gromacs will be truly helpful.
>
>
> Yes and no. The FFT is intrinsically global, and most of the time spent
> doing the PME component of MD is organizing the data to go into the FFT,
> rather than doing the computation. The current implementation of spreading
> charges onto the FFT grid is known to scale poorly across increasing
> numbers of OpenMP cores of an MPI rank. That would be a high-impact problem
> to fix - but start by getting a thorough understanding of the algorithm
> before looking at the code (because the form of the code will not help you
> understand anything). Some profiling with well-targeted function
> instrumentation could be worthwhile here.
>
> Because of this, at scale it is often necessary to use a subset of the MPI
> ranks to handle the PME part, MPMD style (see reference manual, and/or
> GROMACS 4 paper). However, the implementation of that requires that the
> user choose a division in advance, and without running some external
> optimizer (like gmx tune_pme) that choice is difficult because there also
> has to be a PME domain decomposition, and now an extra communication phase
> mapping from one DD to the other, and that can't be efficient unless
> various constraints are satisified... Approaches that would take variables
> out of user space could be quite useful here. For a trivial example, it
> might be best
> * to interleave PME ranks with PP ranks, to spread them out over the
> network to maximize communication bandwidth when doing the all-to-all for
> the 3DFFT, and hopefully minimize communication latency when doing the
> transformation from PP DD to PME DD by having ranks very close, or
> * to pack PME ranks together on the network to minimize external network
> contention during the all-to-all, but to do so in a way that doesn't lose
> all the benefits by instead taking the latency hit at the PP<->PME
> stages...
> Currently the user has to choose one of these "up front." The latter works
> well only in the presence of knowledge about the network topology, which is
> unavailable until someone adds (e.g.) netloc support.
>
> Replacing our home-grown hardware detection support with hwloc support
> would perhaps be higher reward for effort, however.
>
> Avoiding PME entirely is another avenue (but there are two fast-multipole
> projects running here already).
>
> The latest paper
> > on Gromacs 5.0 concludes saying an algorithm implementing preempting fine
> > grained tasks based on priority can lead to improvements. I am also
> trying
> > to look into it and would want to know your take on this.
> >
>
> We don't think the current approach of
>
> 1. spread this task over n threads per rank, then
> 2. do something serial
> 3. spread the next task over the same n threads per rank, then
> 4. do something serial
> 5. spread the next task over the same n threads per rank, then
> ... continue like this
>
> is going to cut it in the long term. You need to be able e.g. to fire off
> the necessary PME communication, then go back to doing bonded work, then 20
> microseconds later when communication arrives drop everything to handle the
> next phase of PME ASAP, then go back to the bondeds, but preferably don't
> trash all your cache in the meantime, e

[gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme 
parameters in the mol2 and frcmod file format. I know that I can generate .itp 
files containing the parameters, which I can later add to my .top file. 
However, it would be much easier to use pdb2gmx directly without stripping the 
heme and the cysteine binding the heme and later manually add it again. I added 
the cysteine to the standard amber force field. However, before adding the heme 
manually I wanted to know if there is a way to load an itp file while executing 
pdb2gmx?

How would you add the information from the cysteine in mol2 format and the heme 
in mol2/frcmod format to amber in gromacs?

Thank you very much,

Max
-- 
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] GROMACS with AMBER heme parameters

[Justin Lemkul]

On 9/25/15 1:32 PM, Ebert Maximilian wrote:

Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again. I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?



pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
ffbonded.itp or ffnonbonded.itp as needed.



How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?



Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is 
already supported via specbond.dat.


-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.

[gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Dear all,
I have a trajectory file generated by gromacs-4.5.5. Recently I tried to
plot radial distribution function using 'gmx rdf' tool available in
gromacs-5.1. But I am getting the following error.
Error in user input:
Invalid command-line options
  In command-line option -f
File 'system.xtc' does not exist or is not accessible.

I knew that gromacs old trajectories can be analysed using new version
tools. But why I am facing this error?


With regards
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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] Analysis of old xtc file using gromacs-5 tools

[Tsjerk Wassenaar]

Hi Venkat,

Does it exist? Is it accessible? The XTC format did not change since the
early years of Gromacs. Can you access it with a different version?

Cheers,

Tsjerk
On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:

> Dear all,
> I have a trajectory file generated by gromacs-4.5.5. Recently I tried to
> plot radial distribution function using 'gmx rdf' tool available in
> gromacs-5.1. But I am getting the following error.
> Error in user input:
> Invalid command-line options
>   In command-line option -f
> File 'system.xtc' does not exist or is not accessible.
>
> I knew that gromacs old trajectories can be analysed using new version
> tools. But why I am facing this error?
>
>
> With regards
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> 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] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi Tsjerk,
Thank you for the quick reply. Yes I can access it with other versions,
like 4.5.5, 5.0.4.

On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar 
wrote:

> Hi Venkat,
>
> Does it exist? Is it accessible? The XTC format did not change since the
> early years of Gromacs. Can you access it with a different version?
>
> Cheers,
>
> Tsjerk
> On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:
>
> > Dear all,
> > I have a trajectory file generated by gromacs-4.5.5. Recently I tried to
> > plot radial distribution function using 'gmx rdf' tool available in
> > gromacs-5.1. But I am getting the following error.
> > Error in user input:
> > Invalid command-line options
> >   In command-line option -f
> > File 'system.xtc' does not exist or is not accessible.
> >
> > I knew that gromacs old trajectories can be analysed using new version
> > tools. But why I am facing this error?
> >
> >
> > With regards
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > 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.
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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] Gromacs says that may GeForce 9800gt is incompatible any help?

[Juliano Braz Carregal]

Gromacs 5 says that may GeForce 9800gt is incompatible any help?
-- 
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] Gromacs says that may GeForce 9800gt is incompatible any help?

[Repic Matej]

Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but 
gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series 
from 2010, but 9800GT is from 2008.

Best,
--
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC – LCBC
BCH 4108
CH - 1015 Lausanne
--

From: 
mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>>
 on behalf of Juliano Braz Carregal 
mailto:julianocarre...@hotmail.com>>
Reply-To: "gmx-us...@gromacs.org" 
mailto:gmx-us...@gromacs.org>>
Date: Friday, September 25, 2015 at 20:46
To: 
"gromacs.org_gmx-users@maillist.sys.kth.se"
 
mailto:gromacs.org_gmx-users@maillist.sys.kth.se>>
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible any 
help?


Gromacs 5 says that may GeForce 9800gt is incompatible any help?
-- 
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] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?

Max

> On Sep 25, 2015, at 1:36 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can generate
>> .itp files containing the parameters, which I can later add to my .top file.
>> However, it would be much easier to use pdb2gmx directly without stripping
>> the heme and the cysteine binding the heme and later manually add it again. I
>> added the cysteine to the standard amber force field. However, before adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>> 
> 
> pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
> ffbonded.itp or ffnonbonded.itp as needed.
> 
>> How would you add the information from the cysteine in mol2 format and the
>> heme in mol2/frcmod format to amber in gromacs?
>> 
> 
> Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys 
> is already supported via specbond.dat.
> 
> -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.

Re: [gmx-users] GROMACS with AMBER heme parameters

[Justin Lemkul]

On 9/25/15 4:22 PM, Ebert Maximilian wrote:

Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?



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

-Justin


Max


On Sep 25, 2015, at 1:36 PM, Justin Lemkul  wrote:



On 9/25/15 1:32 PM, Ebert Maximilian wrote:

Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again. I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?



pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
ffbonded.itp or ffnonbonded.itp as needed.


How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?



Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is 
already supported via specbond.dat.

-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.




--
==

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.

Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

I read that and this is the way I added the cysteine to AMBER which connects to 
the heme. Now I am adding the heme but the FF definition for bonds, angles, etc 
are all in lower case for the GAFF FF. From you answer I guess I need to add 
these lower case atom types and the bonds, angles, etc definition from the GAFF 
FF to the AMBER FF manually.

Not much fun but I will share the work here in the end. Maybe this will help 
people who want to simulate heme containing proteins in GROMACS and 
AMBER99SB-ILDN.

Have a good weekend,
Max


On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 4:22 PM, Ebert Maximilian wrote:
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?


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

-Justin

Max

On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 1:32 PM, Ebert Maximilian wrote:
Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again. I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?


pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
ffbonded.itp or ffnonbonded.itp as needed.

How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?


Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is 
already supported via specbond.dat.

-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.


--
==

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.

Re: [gmx-users] GROMACS with AMBER heme parameters

[Justin Lemkul]

On 9/25/15 4:40 PM, Ebert Maximilian wrote:

I read that and this is the way I added the cysteine to AMBER which connects to 
the heme. Now I am adding the heme but the FF definition for bonds, angles, etc 
are all in lower case for the GAFF FF. From you answer I guess I need to add 
these lower case atom types and the bonds, angles, etc definition from the GAFF 
FF to the AMBER FF manually.



Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, but 
if that residue involves modifications to the force field, then there is more 
work to be done.


-Justin


Not much fun but I will share the work here in the end. Maybe this will help 
people who want to simulate heme containing proteins in GROMACS and 
AMBER99SB-ILDN.

Have a good weekend,
Max


On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 4:22 PM, Ebert Maximilian wrote:
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF 
FF to work in GROMACS? I would need all the bonded and non bonded definitions 
of GAFF for the heme in der AMBER FF port in GROMACS right?


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

-Justin

Max

On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 9/25/15 1:32 PM, Ebert Maximilian wrote:
Hi there,

I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again. I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?


pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
ffbonded.itp or ffnonbonded.itp as needed.

How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?


Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is 
already supported via specbond.dat.

-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.


--
==

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.



--
==

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.

Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

Yeah that is what I thought but that’s life. 

One more question.In the [ atomtypes ] section I need the sigma and epsilon 
value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is in 
nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in 
angstroem and defined as r0 which is sigma *( the 6th root of 2). 

So I picked an atomtype which is defined in the same way in AMBER and GAFF to 
see if I am doing the conversion right. A standard carbon CA is similar in both 
since the definition is taken from OPLS:

GAFF ca  r0: 1.9080  epsilon: 0.0860

If I look in the AMBER FF in GROMACS this changes to 

AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01

If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as 
expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, 
which is half. Why is the sigma value in GROMACS two times the sigma value in 
GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just wanted 
to be sure.

Thanks

> On Sep 25, 2015, at 4:43 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/25/15 4:40 PM, Ebert Maximilian wrote:
>> I read that and this is the way I added the cysteine to AMBER which connects 
>> to the heme. Now I am adding the heme but the FF definition for bonds, 
>> angles, etc are all in lower case for the GAFF FF. From you answer I guess I 
>> need to add these lower case atom types and the bonds, angles, etc 
>> definition from the GAFF FF to the AMBER FF manually.
>> 
> 
> Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, 
> but if that residue involves modifications to the force field, then there is 
> more work to be done.
> 
> -Justin
> 
>> Not much fun but I will share the work here in the end. Maybe this will help 
>> people who want to simulate heme containing proteins in GROMACS and 
>> AMBER99SB-ILDN.
>> 
>> Have a good weekend,
>> Max
>> 
>> 
>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
>> mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
>> Since the heme definition in AMBER uses GAFF atom types how do I get the 
>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded 
>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>> 
>> 
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>> 
>> -Justin
>> 
>> Max
>> 
>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
>> mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can generate
>> .itp files containing the parameters, which I can later add to my .top file.
>> However, it would be much easier to use pdb2gmx directly without stripping
>> the heme and the cysteine binding the heme and later manually add it again. I
>> added the cysteine to the standard amber force field. However, before adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>> 
>> 
>> pdb2gmx does not need .itp information.  grompp does.  Add the parameters to 
>> ffbonded.itp or ffnonbonded.itp as needed.
>> 
>> How would you add the information from the cysteine in mol2 format and the
>> heme in mol2/frcmod format to amber in gromacs?
>> 
>> 
>> Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys 
>> is already supported via specbond.dat.
>> 
>> -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.
>> 
>> 
>> --
>> ==
>> 
>> 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
>> 
>> 

Re: [gmx-users] GROMACS with AMBER heme parameters

[Ebert Maximilian]

I will answer my own question: I found in another post that indeed in GROMACS 
its Rmin. 

Thanks

> On Sep 25, 2015, at 5:25 PM, Ebert Maximilian  wrote:
> 
> Yeah that is what I thought but that’s life. 
> 
> One more question.In the [ atomtypes ] section I need the sigma and epsilon 
> value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is 
> in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in 
> angstroem and defined as r0 which is sigma *( the 6th root of 2). 
> 
> So I picked an atomtype which is defined in the same way in AMBER and GAFF to 
> see if I am doing the conversion right. A standard carbon CA is similar in 
> both since the definition is taken from OPLS:
> 
> GAFF ca  r0: 1.9080  epsilon: 0.0860
> 
> If I look in the AMBER FF in GROMACS this changes to 
> 
> AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01
> 
> If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as 
> expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, 
> which is half. Why is the sigma value in GROMACS two times the sigma value in 
> GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just 
> wanted to be sure.
> 
> Thanks
> 
>> On Sep 25, 2015, at 4:43 PM, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 9/25/15 4:40 PM, Ebert Maximilian wrote:
>>> I read that and this is the way I added the cysteine to AMBER which 
>>> connects to the heme. Now I am adding the heme but the FF definition for 
>>> bonds, angles, etc are all in lower case for the GAFF FF. From you answer I 
>>> guess I need to add these lower case atom types and the bonds, angles, etc 
>>> definition from the GAFF FF to the AMBER FF manually.
>>> 
>> 
>> Indeed, which is what steps 3 and 4 tell you.  Adding a residue is simple, 
>> but if that residue involves modifications to the force field, then there is 
>> more work to be done.
>> 
>> -Justin
>> 
>>> Not much fun but I will share the work here in the end. Maybe this will 
>>> help people who want to simulate heme containing proteins in GROMACS and 
>>> AMBER99SB-ILDN.
>>> 
>>> Have a good weekend,
>>> Max
>>> 
>>> 
>>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul 
>>> mailto:jalem...@vt.edu>> wrote:
>>> 
>>> 
>>> 
>>> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
>>> Since the heme definition in AMBER uses GAFF atom types how do I get the 
>>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded 
>>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>>> 
>>> 
>>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>> 
>>> -Justin
>>> 
>>> Max
>>> 
>>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul 
>>> mailto:jalem...@vt.edu>> wrote:
>>> 
>>> 
>>> 
>>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>>> Hi there,
>>> 
>>> I am trying to simulate a heme containing protein. I found AMBER heme
>>> parameters in the mol2 and frcmod file format. I know that I can generate
>>> .itp files containing the parameters, which I can later add to my .top file.
>>> However, it would be much easier to use pdb2gmx directly without stripping
>>> the heme and the cysteine binding the heme and later manually add it again. 
>>> I
>>> added the cysteine to the standard amber force field. However, before adding
>>> the heme manually I wanted to know if there is a way to load an itp file
>>> while executing pdb2gmx?
>>> 
>>> 
>>> pdb2gmx does not need .itp information.  grompp does.  Add the parameters 
>>> to ffbonded.itp or ffnonbonded.itp as needed.
>>> 
>>> How would you add the information from the cysteine in mol2 format and the
>>> heme in mol2/frcmod format to amber in gromacs?
>>> 
>>> 
>>> Charges and connectivity go in the .rtp entry.  Heme ligation by His and 
>>> Cys is already supported via specbond.dat.
>>> 
>>> -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.
>>> 
>>> 
>>> --
>>> ==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceu

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 137

[Juliano Braz Carregal]

Do you know wich version of gromacs works with this gpu?the page of gromacs says that 9800gt is compatible,but unfortunaly its not true.
Thank you
Em 25/09/2015 5:44 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se escreveu:




Send gromacs.org_gmx-users mailing list submissions to
    gromacs.org_gmx-users@maillist.sys.kth.se

To subscribe or unsubscribe via the World Wide Web, visit
    https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
    gromacs.org_gmx-users-request@maillist.sys.kth.se

You can reach the person managing the list at
    gromacs.org_gmx-users-owner@maillist.sys.kth.se

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

   1. Gromacs says that may GeForce 9800gt is incompatible  any
  help? (Juliano Braz Carregal)
   2. Re: Gromacs says that may GeForce 9800gt is incompatible any
  help? (Repic Matej)
   3. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
   4. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
   5. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
   6. Re: GROMACS with AMBER heme parameters (Justin Lemkul)


--

Message: 1
Date: Fri, 25 Sep 2015 15:46:29 -0300
From: Juliano Braz Carregal 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is
    incompatible    any help?
Message-ID: <SNT406-EAS4017586F92E165604307495B8420@phx.gbl>
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20150925/fcc6225b/attachment-0001.html>

--

Message: 2
Date: Fri, 25 Sep 2015 19:15:43 +
From: Repic Matej 
To: "gmx-users@gromacs.org" 
Subject: Re: [gmx-users] Gromacs says that may GeForce 9800gt is
    incompatible any help?
Message-ID: <D22B692A.12714%matej.repic@epfl.ch>
Content-Type: text/plain; charset="Windows-1252"

Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series from 2010, but 9800GT is from 2008.

Best,
--
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
--

From: > on behalf of Juliano Braz Carregal >
Reply-To: "gmx-users@gromacs.org" >
Date: Friday, September 25, 2015 at 20:46
To: "gromacs.org_gmx-users@maillist.sys.kth.se" >
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible any help?


Gromacs 5 says that may GeForce 9800gt is incompatible any help?


--

Message: 3
Date: Fri, 25 Sep 2015 20:22:54 +
From: Ebert Maximilian 
To: "gmx-users@gromacs.org" 
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <5EF0A589-8604-438C-90ED-55ECB9FC21CE@umontreal.ca>
Content-Type: text/plain; charset="us-ascii"

Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right?

Max

> On Sep 25, 2015, at 1:36 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>> 
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can generate
>> .itp files containing the parameters, which I can later add to my .top file.
>> However, it would be much easier to use pdb2gmx directly without stripping
>> the heme and the cysteine binding the heme and later manually add it again. I
>> added the cysteine to the standard amber force field. However, before adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>> 
> 
> pdb2gmx does not need .itp information.  grompp does.  Add the parameters to ffbonded.itp or ffnonbonded.itp as needed.
> 
>> How would you add the information from the cysteine in mol2 format and the
>> heme in mol2/frcmod format to amber in gromacs?
>> 
> 
> Charges and connectivity go in the .rtp entry.  Heme ligation by His and Cys is already supported via specbond.dat.
> 
> -Justin
> 
> -- 
> 

Re: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible any, help?

[Justin Lemkul]

Please heed this:

> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."


On 9/25/15 5:46 PM, Juliano Braz Carregal wrote:

Do you know wich version of gromacs works with this gpu?the page of gromacs says
that 9800gt is compatible,but unfortunaly its not true.


Presumably you're referring to 
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM which 
is when the only acceleration was provided via OpenMM.  That information is 
outdated by several years.  Moreover, OpenMM (at the time) only supported 
implicit solvent runs with extremely limited features.  You can get version 4.5 
(again, way outdated) and OpenMM-2.0 (if that's even available any more, current 
version is 6.2!) and try to run some limited types of simulations.  But the 
better bet is to get newer hardware and use modern software.


-Justin


Thank you

Em 25/09/2015 5:44 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
escreveu:

Send gromacs.org_gmx-users mailing list submissions to
 gromacs.org_gmx-users@maillist.sys.kth.se

To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
 gromacs.org_gmx-users-requ...@maillist.sys.kth.se

You can reach the person managing the list at
 gromacs.org_gmx-users-ow...@maillist.sys.kth.se

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

1. Gromacs says that may GeForce 9800gt is incompatible  any
   help? (Juliano Braz Carregal)
2. Re: Gromacs says that may GeForce 9800gt is incompatible any
   help? (Repic Matej)
3. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
4. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
5. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
6. Re: GROMACS with AMBER heme parameters (Justin Lemkul)


--

Message: 1
Date: Fri, 25 Sep 2015 15:46:29 -0300
From: Juliano Braz Carregal 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is
 incompatibleany help?
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL:

<http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20150925/fcc6225b/attachment-0001.html>

--

Message: 2
Date: Fri, 25 Sep 2015 19:15:43 +
From: Repic Matej 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] Gromacs says that may GeForce 9800gt is
 incompatible any help?
Message-ID: 
Content-Type: text/plain; charset="Windows-1252"

Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but
gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series
from 2010, but 9800GT is from 2008.

Best,
--
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
--

From:

mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>>
on behalf of Juliano Braz Carregal
mailto:julianocarre...@hotmail.com>>
Reply-To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>"
mailto:gmx-us...@gromacs.org>>
Date: Friday, September 25, 2015 at 20:46
To:

"gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>"

mailto:gromacs.org_gmx-users@maillist.sys.kth.se>>
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible
any help?


Gromacs 5 says that may GeForce 9800gt is incompatible any help?


--

Message: 3
Date: Fri, 25 Sep 2015 20:22:54 +
From: Ebert Maximilian 
To: "gmx-us...@gromacs.org" 
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <5ef0a589-8604-438c-90ed-55ecb9fc2...@umontreal.ca>
Content-Type: text/plain; charset="us-ascii"

Since the heme definition in AMBER uses GAFF atom types how do I get the
GAFF FF to work in GROMACS? I would need all the bonded and non bonded
definitions of GAFF for the heme in der AMBER FF port in GROMACS right?

Max

 > On Sep 25, 2015, at 1:36 PM, Justin Lemkul  wrote:
   

Re: [gmx-users] Regarding gmx-user mailing list thread "Gibbs free energy landscape Vs. the stability of protein structure"

[Naba]

Dear David sir,

Is it feasible to evaluate Gibbs free energy landscape of only the
concerned loops from cartesian coordinates?
I mean to say is it feasible to extract covariance matrix of my concerned
loops from the entire trajectory and then evaluating Gibbs free energy
landscape?
OR, should I extract trajectories of each and every loops separately and
calculating extract covariance matrix of each loop and then should I see
the Gibbs free energy landscape?

On Thu, Sep 24, 2015 at 7:42 PM, David van der Spoel 
wrote:

> On 24/09/15 13:54, Nabajyoti Goswami wrote:
>
>> Sir,
>> I am a very big fan of yours and I deeply apologize for mailing this way.
>> Actually I need some outcome within a very short period of time. So, I
>> could not wait for the mailing lists answers.
>>
>> Coming to the point.. Can you please explain the tricks of dihedral PCA?
>> You answered as my sampling was far from being complete because of the
>> huge differences between my chosen temperatures 300K and 310K, then how
>> can I make some comments at least, if my results are inconclusive. So
>> far as stability point of view, how do I set my MDs?
>>
> As I said you may be sampling different part of phase space, but it could
> also be that it is something very similar in cartesian space.
> The simple recommendation is do not use dihedral PCA at all but something
> in cartesian space.
>
>>
>> I have attached another figure (3D version of the previously generated
>> figure). But I am a bit in confusion to analyze them.
>>
>> Please help a little sir.
>>
>> Regards,
>>
>> Yours truly
>>
>>
>> Nabajyoti Goswami
>>
>> Bioinformatics Infrastructure Facility
>> Department of Animal Biotechnology
>> College of Veterinary Science
>> Assam Agricultural University
>> Khanapara, Guwahati 781022
>> Assam, India
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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.
>



-- 
Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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.