Re: [gmx-users] topology in local?

[Nicola Staffolani]

thank you!


On Wed, May 21, 2014 at 4:10 PM, Justin Lemkul  wrote:

>
>
> On 5/21/14, 9:06 AM, Nicola Staffolani wrote:
>
>> just to improve my knowledge in programming: and I can override it by
>> typing:
>>
>> GMXLIB="address_of_the_new_topology_in_my_computer"
>>
>> right?
>>
>>
> The details depend on your shell.  For csh you need setenv, for bash you
> need export, etc.  Quotes shouldn't be necessary, e.g.:
>
> export GMXLIB=/home/justin/software/gromacs/custom/share/top
>
>
>  But in that case, if I first open a child shell, then the change will be
>> effective only there, and as soon as I come back to the parent shell,
>> GMXLIB will be pointing to the old /usr/share/... address, right?
>> Thank you Justin!
>>
>>
> Any new shell you open will need the environment variable to be set again;
> if it's something you need often (or always) set it in .bashrc, .cshrc, etc.
>
> -Justin
>
>
>  PS I do not think I will try to override it anyway ;) And yes, I manually
>> installed GROMACS because I didn't know I could do it by just using Ubuntu
>> Software Center...
>>
>>
>> On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/21/14, 8:38 AM, Nicola Staffolani wrote:
>>>
>>>  and so how do I make GMXLIB point to somewhere else than
 /usr/share/gromacs/top?


  If Gromacs is installed in /usr/share/gromacs, that's where it should
>>> point. Otherwise, just override it by setting $GMXLIB in your shell
>>> however
>>> you like. Hopefully it won't break anything by doing that.
>>>
>>> -Justin
>>>
>>>
>>>
>>>  On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury >>>
> wrote:
>

   On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani

> wrote:
>
>   Dear Chandan,
>
>>
>> thank you for your reply. Anyway, before making any change to my
>> GROMACS
>> and therefore risking  to "destroy", can I ask again your advice?
>>
>>   Sure.
>>
>
>
>From what I have read about environment
>> variables,
>> if another simulation is already running on a computer and I want to
>> launch
>> my simulation but using a different topology, and if my new topology
>> is
>> stored in the directory somewhere/my_topology, then I should send the
>> following command (for example for a md.com command):
>>
>> $GMXLIB=somewhere/my_topology md.com
>>
>> Right?
>>
>> And is it true that the by doing so, I will affect only this
>> simulation,
>> i.e. I will have changed the path to the topology only for this run,
>>
>>  while
>
>  for all the next ones the old path (/usr/share/gromacs/top) will be
>> kept?
>>
>>
>>   I do not understand where your confusion lies. BTW, Gromacs works in
>>
> the
> following way:
> 1. pdb2gmx  generates the topolopy file (human readable).
> 2. grompp reads this topology and the structure file to generate a tpr
> (binary
> file).
> In the process of generating the tpr file, it reads the force field
> (FF)
> files. The location of the FF is taken from the GMXLIB variable. GMXLIB
> may
> point to any path of the computer where the FF is kept.
> 3. You can use this tpr file, to run your simulation to which every
> computer you want (gmx should be installed).
> If a simulation is already running, then your simulation would take
> more
> time to complete. Your tpr file will not be affected by the previous
> simulation.
>
> The same is also told by Justin.
>
> Thank you,
>
>
>> Nicola
>>
>> --
>>
>>  Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> 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.
>
>
>


  --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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)subscr

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Vito Genna]

Dear Dr. Warrem, Dear Tsjerk,

Thank you for your emails.
Following the suggestion of Dr. Warren I created several dir in which I applied 
different protocols on my system

-- DIR1 --

 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump  (output 
System)

 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n 
iindex.ndx (centering all the frames on Protein)   (output system)
 
 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur 
rect (output System)

The related Figures are in the following link: 
http://wikisend.com/download/832038/Figtest1.zip

#Comment: I obtain the same result also if a change rect with compact in the 
third step.

-- DIR2 --

 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump  (output 
System)

 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n 
iindex.ndx (centering all the frames on Protein)   (output system)
 
 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur 
rect (output System)

 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive 
(fitting on Protein)

The pics are here: http://wikisend.com/download/615140/FigTest2.zip

#Comment: Here again, I obtain the same results as in the DIR1 but My protein 
has not translational motions.
#Comment: In the step 2 i also centered the system on the Protein_DNA, nothing 
changes.


Then, I tried different pbc/centering combination again but I strongly believe 
that fixing DNA-Protein complex is enough to obtain a good system.

What would do you do to bring back the dsDNA inside the protein?
In which step would you operate your command?

Thanks in advance for your time.

Cheers


V 




Vito Genna, PhD-Fellow
Italian Institute of Technology
Drug Discovery and Development department
Via Morego 30, 16163 Genoa, Italy

-
The process of scientific discovery is, in effect, a continual flight from 
wonder.
Albert Einstein



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas Warren 
[dallas.war...@monash.edu]
Sent: Thursday, May 22, 2014 1:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for 
VMD using

Would suggest that each time you try a different workflow, do so in a new 
subdirectory and copy the required files into there.  That way you ensure are 
using the files you think that you are.

Will help those assisting to then post an image of the coordinate files at each 
step of the work flow, to see how things are changing, or not.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

> -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
> Vito Genna
> Sent: Wednesday, 21 May 2014 11:07 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> problems for VMD using
>
> Dear Tsjerk,
>
> No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png)
> I think that the first step need to be changed that's why I tried (whit
> no success)
> the flag -pbc whole. I'm still looking for a solution.
>
> Thanks again.
>
> V
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
> ---
> --
> The process of scientific discovery is, in effect, a continual flight
> from wonder.
> Albert Einstein
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
> Wassenaar [tsje...@gmail.com]
> Sent: Wednesday, May 21, 2014 1:48 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> problems for VMD using
>
> Hey Vito,
>
> After the first step, does the trajectory (say the last frame) look
> fine?
> If it does (everything nicely assembled), then after the second step,
> does
> it still look fine, and is it placed properly in the center of the box?
>
> Cheers,
>
> Tsjerk
>
>
> On Wed, May 21, 2014 at 12:50 PM, Vito Genna  wrote:
>
> > Hi Tsierk,
> >
> > Ok.
> >
> > 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> > (output System)
> >
> > 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -
> center -n
> > ind

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Tsjerk Wassenaar]

Hi Vito,

Does npt.tpr correspond to the first frame of the trajectory and is the
structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
frame in which the complex is separated is if the reference structure has
them already separated. In that case, nothing you'll try will give you what
you want. What I do in such cases is dump the first frame, using -pbc
whole, and then shift the chains in Pymol according to the box vectors to
have them together. Then I use the resulting structure as reference for
processing the trajectory.

Cheers,

Tsjerk


On Thu, May 22, 2014 at 10:59 AM, Vito Genna  wrote:

> Dear Dr. Warrem, Dear Tsjerk,
>
> Thank you for your emails.
> Following the suggestion of Dr. Warren I created several dir in which I
> applied different protocols on my system
>
> -- DIR1 --
>
>  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
>  (output System)
>
>  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> -n iindex.ndx (centering all the frames on Protein)   (output system)
>
>  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol
> -ur rect (output System)
>
> The related Figures are in the following link:
> http://wikisend.com/download/832038/Figtest1.zip
>
> #Comment: I obtain the same result also if a change rect with compact in
> the third step.
>
> -- DIR2 --
>
>  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
>  (output System)
>
>  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> -n iindex.ndx (centering all the frames on Protein)   (output system)
>
>  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol
> -ur rect (output System)
>
>  4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit
> progressive (fitting on Protein)
>
> The pics are here: http://wikisend.com/download/615140/FigTest2.zip
>
> #Comment: Here again, I obtain the same results as in the DIR1 but My
> protein has not translational motions.
> #Comment: In the step 2 i also centered the system on the Protein_DNA,
> nothing changes.
>
>
> Then, I tried different pbc/centering combination again but I strongly
> believe that fixing DNA-Protein complex is enough to obtain a good system.
>
> What would do you do to bring back the dsDNA inside the protein?
> In which step would you operate your command?
>
> Thanks in advance for your time.
>
> Cheers
>
>
> V
>
>
>
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
>
> -
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas
> Warren [dallas.war...@monash.edu]
> Sent: Thursday, May 22, 2014 1:40 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Would suggest that each time you try a different workflow, do so in a new
> subdirectory and copy the required files into there.  That way you ensure
> are using the files you think that you are.
>
> Will help those assisting to then post an image of the coordinate files at
> each step of the work flow, to see how things are changing, or not.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> > -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
> > Vito Genna
> > Sent: Wednesday, 21 May 2014 11:07 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> > problems for VMD using
> >
> > Dear Tsjerk,
> >
> > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png)
> > I think that the first step need to be changed that's why I tried (whit
> > no success)
> > the flag -pbc whole. I'm still looking for a solution.
> >
> > Thanks again.
> >
> > V
> >
> > Vito Genna, PhD-Fellow
> > Italian Institute of Technology
> > Drug Discovery and Development department
> > Via Morego 30, 16163 Genoa, Italy
> >
> > ---
> > --
> > The process of scientific discovery is, in effect, a continual flight
> > from wonder.
> > Albert Einstein
> >
> >
> > 

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Vito Genna]

Dear Tsjerk,

I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely 
assembled system (npt.pdb).

Well, my system start to cross the boundaries after 20 ns of production phase 
so the npt.tpr is not
the first frame of the trajectories that I trying to fix. 

After your email I've generated the md_0_1.tpr respecting your request with the 
command  editconf -f md_0_1.tpr -o md_0_1.pdb
and again I obtain a well assembled system.

The trajectories that I want to fix, is obtained from: trjconv_mpi -f 
md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100

To be consistent in the procedure, I did again all the steps (-pbc nojump, 
-center, -compact -ur rect) using the md_0_1.tpr.

The result is exactly the same! I'm really losing hope!

I will try the Pymol strategy also.

Thank you for your hints.

Cheers

V



Vito Genna, PhD-Fellow
Italian Institute of Technology
Drug Discovery and Development department
Via Morego 30, 16163 Genoa, Italy

-
The process of scientific discovery is, in effect, a continual flight from 
wonder.
Albert Einstein



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk 
Wassenaar [tsje...@gmail.com]
Sent: Thursday, May 22, 2014 11:10 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for 
VMD using

Hi Vito,

Does npt.tpr correspond to the first frame of the trajectory and is the
structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
frame in which the complex is separated is if the reference structure has
them already separated. In that case, nothing you'll try will give you what
you want. What I do in such cases is dump the first frame, using -pbc
whole, and then shift the chains in Pymol according to the box vectors to
have them together. Then I use the resulting structure as reference for
processing the trajectory.

Cheers,

Tsjerk


On Thu, May 22, 2014 at 10:59 AM, Vito Genna  wrote:

> Dear Dr. Warrem, Dear Tsjerk,
>
> Thank you for your emails.
> Following the suggestion of Dr. Warren I created several dir in which I
> applied different protocols on my system
>
> -- DIR1 --
>
>  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
>  (output System)
>
>  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> -n iindex.ndx (centering all the frames on Protein)   (output system)
>
>  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol
> -ur rect (output System)
>
> The related Figures are in the following link:
> http://wikisend.com/download/832038/Figtest1.zip
>
> #Comment: I obtain the same result also if a change rect with compact in
> the third step.
>
> -- DIR2 --
>
>  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
>  (output System)
>
>  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> -n iindex.ndx (centering all the frames on Protein)   (output system)
>
>  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol
> -ur rect (output System)
>
>  4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit
> progressive (fitting on Protein)
>
> The pics are here: http://wikisend.com/download/615140/FigTest2.zip
>
> #Comment: Here again, I obtain the same results as in the DIR1 but My
> protein has not translational motions.
> #Comment: In the step 2 i also centered the system on the Protein_DNA,
> nothing changes.
>
>
> Then, I tried different pbc/centering combination again but I strongly
> believe that fixing DNA-Protein complex is enough to obtain a good system.
>
> What would do you do to bring back the dsDNA inside the protein?
> In which step would you operate your command?
>
> Thanks in advance for your time.
>
> Cheers
>
>
> V
>
>
>
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
>
> -
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas
> Warren [dallas.war...@monash.edu]
> Sent: Thursday, May 22, 2014 1:40 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Would suggest that each time you try a different workflow, do so in a new
> subdirectory and copy the required files into there.  That way you ensure
> are using the files you think that you are.

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Tsjerk Wassenaar]

Hey Vito,

Don't use -skip. And add -pbc nojump to that first run of trjconv:

trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump

Then have a look at the last frame to see if it's good. If md_0_1.tpr is
assembled properly, then the last frame should be too, provided the
assembly did not fall apart (in which case you're in real trouble).

Cheers,

Tsjerk



On Thu, May 22, 2014 at 3:01 PM, Vito Genna  wrote:

> Dear Tsjerk,
>
> I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely
> assembled system (npt.pdb).
>
> Well, my system start to cross the boundaries after 20 ns of production
> phase so the npt.tpr is not
> the first frame of the trajectories that I trying to fix.
>
> After your email I've generated the md_0_1.tpr respecting your request
> with the command  editconf -f md_0_1.tpr -o md_0_1.pdb
> and again I obtain a well assembled system.
>
> The trajectories that I want to fix, is obtained from: trjconv_mpi -f
> md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100
>
> To be consistent in the procedure, I did again all the steps (-pbc nojump,
> -center, -compact -ur rect) using the md_0_1.tpr.
>
> The result is exactly the same! I'm really losing hope!
>
> I will try the Pymol strategy also.
>
> Thank you for your hints.
>
> Cheers
>
> V
>
>
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
>
> -
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
> Wassenaar [tsje...@gmail.com]
> Sent: Thursday, May 22, 2014 11:10 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Hi Vito,
>
> Does npt.tpr correspond to the first frame of the trajectory and is the
> structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
> npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
> frame in which the complex is separated is if the reference structure has
> them already separated. In that case, nothing you'll try will give you what
> you want. What I do in such cases is dump the first frame, using -pbc
> whole, and then shift the chains in Pymol according to the box vectors to
> have them together. Then I use the resulting structure as reference for
> processing the trajectory.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, May 22, 2014 at 10:59 AM, Vito Genna  wrote:
>
> > Dear Dr. Warrem, Dear Tsjerk,
> >
> > Thank you for your emails.
> > Following the suggestion of Dr. Warren I created several dir in which I
> > applied different protocols on my system
> >
> > -- DIR1 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc
> mol
> > -ur rect (output System)
> >
> > The related Figures are in the following link:
> > http://wikisend.com/download/832038/Figtest1.zip
> >
> > #Comment: I obtain the same result also if a change rect with compact in
> > the third step.
> >
> > -- DIR2 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc
> mol
> > -ur rect (output System)
> >
> >  4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit
> > progressive (fitting on Protein)
> >
> > The pics are here: http://wikisend.com/download/615140/FigTest2.zip
> >
> > #Comment: Here again, I obtain the same results as in the DIR1 but My
> > protein has not translational motions.
> > #Comment: In the step 2 i also centered the system on the Protein_DNA,
> > nothing changes.
> >
> >
> > Then, I tried different pbc/centering combination again but I strongly
> > believe that fixing DNA-Protein complex is enough to obtain a good
> system.
> >
> > What would do you do to bring back the dsDNA inside the protein?
> > In which step would you operate your command?
> >
> > Thanks in advance for your time.
> >
> > Cheers
> >
> >
> > V
> >
> >
> >
> >
> > Vito Genna, PhD-Fellow
> > Italian Institute of Technology
> > Drug Discovery and Development department
> > Via Morego 30, 16163 Genoa, Italy
> >
> >
> >
> -

[gmx-users] Gromacs for reverse transformation

[shivangi nangia]

Hello,

I want to do a reverse transformation of my system containing: bi-layer,
protein and water.

The Martini website (
http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to
install gromacs version 3.3.1

I am currently using 4.6.1 gromacs version.

ques A: Is this version incapable of the transformation?

Also, the martini website says to:

*"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
contains all necessary gromacs files for this exercise.*

*2. Compile and/or source the modifi ed version of gromacs (remember this
tool is based upon gromacs version 3.3.1 and needs the corresponding tricks
and threats to be compiled.)*

*source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*


ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL
directory
ques C: On performing untar on gmx_rev.tar.gz there is no bin folder

KIndly help.

Thanks,
sxn
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[gmx-users] RDF of solvation shell molecules

[sujithkakkat .]

Hello,

I would like to know if it is possible to plot the RDF of water
molecules belonging to the solvation shell of a solute. I mean, I want to
know the effect of the solute on the water arrangement in the solvation
shell.  Is there a way to do this?

Regards,

Sujith.
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Re: [gmx-users] 答复: about exchange replica with replicas 140

[HANNIBAL LECTER]

Did you check the .err file as well? What does it say?

How many cores do each node in the HPC have? There might be some issues
with the supercomputer that you may be using? One of the nodes might have
some issues which is probably causing the problem?

I have used > 300 cores for replica exchange simulations without any issues.


On Thu, May 22, 2014 at 12:47 AM, #ZHANG HAIPING# wrote:

> Dear Justin:
> The scripts I used is as follow:
> ## Set job parameters
>
> ## Job Name
> #BSUB -J OpenMPI
>
> ## Queue  Name
> #BSUB -q medium_priority
>
> ## Output and Input Errors
> #BSUB -o job%J.out
> #BSUB -e job%J.err
>
> ## Specify walltime in HH:MM
> #BSUB -W 60:00
>
> ## 16 Processors per Host
> #BSUB -R "span[ptile=16]"
>
> ## Requesting for 32 cores
> #BSUB -n 140
>
> # Need to make our own machinefile
> MACHINEFILE=mymacs.$LSB_JOBID
> for i in `echo $LSB_HOSTS`
> do
> echo $i
> done > $MACHINEFILE
>
>
> ## load module enviroement
> module load openmpi-1.6.5-intel-v12.1.5
> module load intel-12.1.5
>
> ## Run mpi program
> cd /gpfs/home/hzhang020/REMD/remdrun/scratch
> /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core
> --report-bindings  -np 140 -machinefile $MACHINEFILE
> /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s
> prefix_.tpr -multi 140   -replex 3000
>
>
> There was not obvious error information, just have the output file size is
> always 0. After long time, I kill it myself.
>
>
> NOTE: The load imbalance in PME FFT and solve is 384%.
>   For optimal PME load balancing
>   PME grid_x (1728) and grid_y (1728) should be divisible by
> #PME_nodes_x (2)
>   and PME grid_y (1728) and grid_z (1728) should be divisible by
> #PME_nodes_y (1)
>
>
> NOTE: The load imbalance in PME FFT and solve is 384%.
>   For optimal PME load balancing
>   PME grid_x (1728) and grid_y (1728) should be divisible by
> #PME_nodes_x (2)
>   and PME grid_y (1728) and grid_z (1728) should be divisible by
> #PME_nodes_y (1)
>
> --
> WARNING: A process refused to die!
>
> Host: comp094
> PID:  6751
>
> This process may still be running and/or consuming resources.
>
> --
> --
> mpirun noticed that process rank 273 with PID 30914 on node comp122 exited
> on signal 9 (Killed).
> --
>
>
>
>
> 
> 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> 代表 Justin Lemkul <
> jalem...@vt.edu>
> 发送时间: 2014年5月22日 10:57
> 收件人: gmx-us...@gromacs.org
> 主题: Re: [gmx-users] about  exchange replica with  replicas 140
>
> On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote:
> > Dear gromacs user:
> >
> > I have encounter a problem when used HPC(high performance computer) to
> run replica exchange. I find that when I used replica over 128, it will not
> work, while under 128 , it is ok, even when I used cores much more than
> 128(several cores for one replica). The version  I used is
> gromacs-4.6.2-double-intel. Hope for you help.
> >
>
> You need to provide more information.  Specifically, what commands are you
> issuing?  What does "will not work" mean?  Is there a specific error you
> are
> getting?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Nanoparticle topology

[HANNIBAL LECTER]

Parameters for metals are readily available in various forcefields in
Gromacs. If your nanoparticles are gold spheres suspended freely in the
system, then you can just get the parameters from from the forcefield files
and specify the number of gold atoms in the topology file.


On Wed, May 21, 2014 at 9:34 PM, guhansingh  wrote:

> Dear sir,
> I need to simulate gold nanoparticles (*NP*) interaction with some ligands
> (drugs). I can get ligand topology via ATB/ Prodrug server, but I can't get
> nanoparticle topology. Is there any external tools for *NP* modelling and
> topology generation.? Any other modifications to simulate metal atoms via
> GROMACS.?
> Thanks in advance
>
> --
> Guhan.KA
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Re: [gmx-users] (no subject)

[HANNIBAL LECTER]

You should provide with more information. The error message clearly states
that there are multiple definitions for the moleculetype CU1. You should
check carefully for redundancies in the top file


On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput
wrote:

> dear gromacs users
> I tried to add ions to my .gro file as it was showing the warning that:-
> System has non zero charge.
> But a new error occured when i run grompp command again:-
>  Program grompp_d, VERSION 4.6.3
> Source code file: /build/buildd/gromacs-4.6.3/src/kernel/toppush.c, line:
> 1412
>
> Fatal error:
> moleculetype CU1 is redefined
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Please help me...
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Re: [gmx-users] Gromacs for reverse transformation

[Tsjerk Wassenaar]

Hi sxn,

I would argue that that method for reverse transformation is largely
obsolete. Please have a look at
http://www.cgmartini.nl/cgmartini/index.php/back

Cheers,

Tsjerk


On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
wrote:

> Hello,
>
> I want to do a reverse transformation of my system containing: bi-layer,
> protein and water.
>
> The Martini website (
> http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to
> install gromacs version 3.3.1
>
> I am currently using 4.6.1 gromacs version.
>
> ques A: Is this version incapable of the transformation?
>
> Also, the martini website says to:
>
> *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
> contains all necessary gromacs files for this exercise.*
>
> *2. Compile and/or source the modifi ed version of gromacs (remember this
> tool is based upon gromacs version 3.3.1 and needs the corresponding tricks
> and threats to be compiled.)*
>
> *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
>
>
> ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL
> directory
> ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
>
> KIndly help.
>
> Thanks,
> sxn
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

[Vito Genna]

Dear Tsjerk,

I'm glad to write to you because it works fine! 
The system is now perfectly assemble. -pbc nojump using the md_0_1.tpr is enough
to rebuild the system. The only problem is the water that diffuses leaving the 
protein.
I think that with the -center flag i can bring back H20 inside the box.

Thank you so much! I was doing a lot of attempts!

Cheers

Vito

Vito Genna, PhD-Fellow
Italian Institute of Technology
Drug Discovery and Development department
Via Morego 30, 16163 Genoa, Italy

-
The process of scientific discovery is, in effect, a continual flight from 
wonder.
Albert Einstein



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk 
Wassenaar [tsje...@gmail.com]
Sent: Thursday, May 22, 2014 4:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for 
VMD using

Hey Vito,

Don't use -skip. And add -pbc nojump to that first run of trjconv:

trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump

Then have a look at the last frame to see if it's good. If md_0_1.tpr is
assembled properly, then the last frame should be too, provided the
assembly did not fall apart (in which case you're in real trouble).

Cheers,

Tsjerk



On Thu, May 22, 2014 at 3:01 PM, Vito Genna  wrote:

> Dear Tsjerk,
>
> I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely
> assembled system (npt.pdb).
>
> Well, my system start to cross the boundaries after 20 ns of production
> phase so the npt.tpr is not
> the first frame of the trajectories that I trying to fix.
>
> After your email I've generated the md_0_1.tpr respecting your request
> with the command  editconf -f md_0_1.tpr -o md_0_1.pdb
> and again I obtain a well assembled system.
>
> The trajectories that I want to fix, is obtained from: trjconv_mpi -f
> md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100
>
> To be consistent in the procedure, I did again all the steps (-pbc nojump,
> -center, -compact -ur rect) using the md_0_1.tpr.
>
> The result is exactly the same! I'm really losing hope!
>
> I will try the Pymol strategy also.
>
> Thank you for your hints.
>
> Cheers
>
> V
>
>
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
>
> -
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
> Wassenaar [tsje...@gmail.com]
> Sent: Thursday, May 22, 2014 11:10 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Hi Vito,
>
> Does npt.tpr correspond to the first frame of the trajectory and is the
> structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
> npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
> frame in which the complex is separated is if the reference structure has
> them already separated. In that case, nothing you'll try will give you what
> you want. What I do in such cases is dump the first frame, using -pbc
> whole, and then shift the chains in Pymol according to the box vectors to
> have them together. Then I use the resulting structure as reference for
> processing the trajectory.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, May 22, 2014 at 10:59 AM, Vito Genna  wrote:
>
> > Dear Dr. Warrem, Dear Tsjerk,
> >
> > Thank you for your emails.
> > Following the suggestion of Dr. Warren I created several dir in which I
> > applied different protocols on my system
> >
> > -- DIR1 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc
> mol
> > -ur rect (output System)
> >
> > The related Figures are in the following link:
> > http://wikisend.com/download/832038/Figtest1.zip
> >
> > #Comment: I obtain the same result also if a change rect with compact in
> > the third step.
> >
> > -- DIR2 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc 

Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning

[Thomas C. O'Connor]

Hey,

Yes, everything runs fine if I work on one node with one or more GPU's. The
crash occurs, similar to the previous mailing list post:

http://comments.gmane.org/gmane.science.biology.gromacs.user/63911

It crashes when we attempt to work across multiple GPU enabled nodes. This
happens when our cluster of C2050's is used but not when our nodes with
K20's are used. The CPU architecture on the two node types are also
slightly different but both are Intel hardware.

Hopefully there is a solution.

Thanks for the tips on launch configurations. I think my simulations are
scaling pretty well with the GPU's.  I'm working with a dense city of many
millions of atoms.


On Wed, May 21, 2014 at 8:52 PM, Szilárd Páll wrote:

> Hi,
>
> Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a
> single GPU? How about two?
>
> Btw, unless you have some rather exotic setup, you won't be able to
> get much improvement from using more than three, at most four GPUs per
> node - you need CPU cores to match them (and a large system to deed
> the GPUs and scale). Multi runs could work well, though.
>
> Cheers,
>
>
> --
> Szilárd
>
>
> On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor 
> wrote:
> > Hey Folks,
> >
> > I'm attempting to run simulations on a multi-node gpu cluster and my
> > simulations are crashing after flagging a open-mpi fork() warning:
> >
> >
> *--*
> > *An MPI process has executed an operation involving a call to the*
> > *"fork()" system call to create a child process.  Open MPI is currently*
> > *operating in a condition that could result in memory corruption or*
> > *other system errors; your MPI job may hang, crash, or produce silent*
> > *data corruption.  The use of fork() (or system() or other calls that*
> > *create child processes) is strongly discouraged.*
> >
> > *The process that invoked fork was:*
> >
> > *  Local host:  lngpu019 (PID 11549)*
> > *  MPI_COMM_WORLD rank: 18*
> >
> > *If you are *absolutely sure* that your application will successfully*
> > *and correctly survive a call to fork(), you may disable this warning*
> > *by setting the mpi_warn_on_fork MCA parameter to 0.*
> >
> *--*
> >
> >
> > I saw a similar mailing-list post about this sort of issue from September
> > 2013, but the thread had no resolution.
> >
> >
> >- Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla
> >C2050 GPU's.
> >
> >
> >- we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi
> >
> >
> >- I compiled GROMACS on one of the compute nodes with the C2050's.
> >
> > We also have a few nodes with newer K20 NVIDIA GPU's. When we compile
> > GROMACS on these nodes we can run the code across multiple nodes and
> GPU's
> > without any errors.
> >
> > I don't know if the fork() error is directly related to the crash or not;
> > or if there might be obscure, device specific object files outside my
> build
> > directory, that I should delete. Any insight you folks could provide to
> > help me solve this issue would be appreciated.
> >
> > Thanks,
> >
> >
> > --
> > Thomas O'Connor
> > Graduate Research Assistant
> > MCS IGERT Fellow
> >
> > Department of Physics & Astronomy
> > The Johns Hopkins University
> > 3701 San Martin Drive
> > Baltimore, MD 21218*tocon...@jhu.edu *410.516.8587
> > --
> > Gromacs Users mailing list
> >
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> posting!
> >
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>



-- 
Thomas O'Connor
Graduate Research Assistant
MCS IGERT Fellow

Department of Physics & Astronomy
The Johns Hopkins University
3701 San Martin Drive
Baltimore, MD 21218*tocon...@jhu.edu *410.516.8587
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[gmx-users] BCAM Internship Position Announcement

[Bruno Escribano]

The following BCAM Internship position is open at BCAM – Basque Center for 
Applied Mathematics, an interdisciplinary research center located in Bilbao. 
 
The interested applicants can apply via the following webpage:
http://www.bcamath.org/en/research/internships
 
INTERNSHIP DATA
 
Research topic title:
Free energy calculations using molecular dynamics and Markov chain Monte Carlo 
methods
 
Research topic description:
Study, implementation and testing of Monte Carlo techniques combined with 
classical molecular dynamics (MD) with the ultimate objective of calculating 
protein binding energies ΔG. The project will result in a new simulation 
method based on the adaptation of the existing Generalized Shadow Hybrid Monte 
Carlo (GSHMC) to umbrella sampling.
 
The tasks to be performed by the intern involve:
- modifying the open-source software MD package GROMACS
- setting up and running simulations of biomolecular systems using the modified 
software on parallel computational servers
- analysing results and calculating ΔG using the potential of mean force curve
 
Keywords:
Molecular Dynamics, Hybrid Monte Carlo, Umbrella sampling, Hamiltonian 
dynamics
 
Required knowledge and skills:
Hamiltonian dynamics, Monte Carlo sampling, C programming, Unix/Linux
 
Required language skills:
English
 
Duration and dates:
2-3 months during 2014
 
Application deadline:
June 1st, 2014
 
Supervisor:
Bruno Escribano and Elena Akhmatskaya
 
Research line:
Modelling and Simulation in Life and Materials Sciences - M3A Research Area
 
---
Bruno Escribano
BCAM Researcher
BCAM – Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao - Basque Country - Spain
Tel. +34 946 567 853
bescrib...@bcamath.org | www.bcamath.org
( matematika mugaz bestalde )
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Re: [gmx-users] RDF of solvation shell molecules

[Chandan Choudhury]

Hi Sujith,

g_rdf is the tool you need.

Chandan


On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . wrote:

> Hello,
>
> I would like to know if it is possible to plot the RDF of water
> molecules belonging to the solvation shell of a solute. I mean, I want to
> know the effect of the solute on the water arrangement in the solvation
> shell.  Is there a way to do this?
>
> Regards,
>
> Sujith.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
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Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning

[Mark Abraham]

On Thu, May 22, 2014 at 5:31 PM, Thomas C. O'Connor wrote:

> Hey,
>
> Yes, everything runs fine if I work on one node with one or more GPU's. The
> crash occurs, similar to the previous mailing list post:
>
> http://comments.gmane.org/gmane.science.biology.gromacs.user/63911
>
> It crashes when we attempt to work across multiple GPU enabled nodes. This
> happens when our cluster of C2050's is used but not when our nodes with
> K20's are used. The CPU architecture on the two node types are also
> slightly different but both are Intel hardware.
>

I would suspect a difference in CUDA version, CUDA driver version, or MPI
version could be the origin here (see top of mdrun log file for some
information here). Normal use of mdrun does not use system() or fork() or
make child processes, which is the basis for my suspicion that the problem
is not within GROMACS. If there's a way to run some other MPI+GPU code on
the machine, whether it works might be useful information. Running mdrun
within a debugger will permit you to observe whether the crash is before
mdrun starts, or not.


> Hopefully there is a solution.
>
> Thanks for the tips on launch configurations. I think my simulations are
> scaling pretty well with the GPU's.  I'm working with a dense city of many
> millions of atoms.
>

Good, you'd want to be doing something like that.

Mark


>
> On Wed, May 21, 2014 at 8:52 PM, Szilárd Páll  >wrote:
>
> > Hi,
> >
> > Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a
> > single GPU? How about two?
> >
> > Btw, unless you have some rather exotic setup, you won't be able to
> > get much improvement from using more than three, at most four GPUs per
> > node - you need CPU cores to match them (and a large system to deed
> > the GPUs and scale). Multi runs could work well, though.
> >
> > Cheers,
> >
> >
> > --
> > Szilárd
> >
> >
> > On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor 
> > wrote:
> > > Hey Folks,
> > >
> > > I'm attempting to run simulations on a multi-node gpu cluster and my
> > > simulations are crashing after flagging a open-mpi fork() warning:
> > >
> > >
> >
> *--*
> > > *An MPI process has executed an operation involving a call to the*
> > > *"fork()" system call to create a child process.  Open MPI is
> currently*
> > > *operating in a condition that could result in memory corruption or*
> > > *other system errors; your MPI job may hang, crash, or produce silent*
> > > *data corruption.  The use of fork() (or system() or other calls that*
> > > *create child processes) is strongly discouraged.*
> > >
> > > *The process that invoked fork was:*
> > >
> > > *  Local host:  lngpu019 (PID 11549)*
> > > *  MPI_COMM_WORLD rank: 18*
> > >
> > > *If you are *absolutely sure* that your application will successfully*
> > > *and correctly survive a call to fork(), you may disable this warning*
> > > *by setting the mpi_warn_on_fork MCA parameter to 0.*
> > >
> >
> *--*
> > >
> > >
> > > I saw a similar mailing-list post about this sort of issue from
> September
> > > 2013, but the thread had no resolution.
> > >
> > >
> > >- Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla
> > >C2050 GPU's.
> > >
> > >
> > >- we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi
> > >
> > >
> > >- I compiled GROMACS on one of the compute nodes with the C2050's.
> > >
> > > We also have a few nodes with newer K20 NVIDIA GPU's. When we compile
> > > GROMACS on these nodes we can run the code across multiple nodes and
> > GPU's
> > > without any errors.
> > >
> > > I don't know if the fork() error is directly related to the crash or
> not;
> > > or if there might be obscure, device specific object files outside my
> > build
> > > directory, that I should delete. Any insight you folks could provide to
> > > help me solve this issue would be appreciated.
> > >
> > > Thanks,
> > >
> > >
> > > --
> > > Thomas O'Connor
> > > Graduate Research Assistant
> > > MCS IGERT Fellow
> > >
> > > Department of Physics & Astronomy
> > > The Johns Hopkins University
> > > 3701 San Martin Drive
> > > Baltimore, MD 21218*tocon...@jhu.edu *410.516.8587
> > > --
> > > 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

[gmx-users] Postdoctoral Fellowship in Energy Storage

[Bruno Escribano]

Dear colleagues,
 
the Basque Center for Applied Mathematics and CIC energiGUNE are announcing a 
joint postdoctoral fellowship. The project involves a combination of classical 
molecular dynamics and ab initio calculations. The project is ideal for a 
candidate with a strong background and interest in method development and 
advanced materials simulation. The successful candidate will work on atomic-
level simulations of ion insertion in electrode nanomaterials for rechargeable 
batteries.
 
Here is the link to the position announcement:
 
http://www.bcamath.org/documentos_public/archivos/ofertas/PostDocProfile_BCAM-
CICenergiGUNE.pdf
 
Please fell free to pass this information to potentially interested people.
 
 
Best regards,
 
Bruno Escribano
BCAM Researcher
BCAM – Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao - Basque Country - Spain
Tel. +34 946 567 842
bescrib...@bcamath.org | www.bcamath.org
( matematika mugaz bestalde )
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Re: [gmx-users] Gromacs for reverse transformation

[Chandan Choudhury]

Hi Tsjerk,
Do the scripts available in the backward.zip file
http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help
me to backmap a coarse-grained polymer?

Chandan


On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar  wrote:

> Hi sxn,
>
> I would argue that that method for reverse transformation is largely
> obsolete. Please have a look at
> http://www.cgmartini.nl/cgmartini/index.php/back
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> wrote:
>
> > Hello,
> >
> > I want to do a reverse transformation of my system containing: bi-layer,
> > protein and water.
> >
> > The Martini website (
> > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says
> to
> > install gromacs version 3.3.1
> >
> > I am currently using 4.6.1 gromacs version.
> >
> > ques A: Is this version incapable of the transformation?
> >
> > Also, the martini website says to:
> >
> > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
> > contains all necessary gromacs files for this exercise.*
> >
> > *2. Compile and/or source the modifi ed version of gromacs (remember this
> > tool is based upon gromacs version 3.3.1 and needs the corresponding
> tricks
> > and threats to be compiled.)*
> >
> > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> >
> >
> > ques B:On performing untar on rev_trans.tar.gz there is no
> MARTINITUTORIAL
> > directory
> > ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
> >
> > KIndly help.
> >
> > Thanks,
> > sxn
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
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[gmx-users] 答复: 答复: about exchange replica with replicas 140

[#ZHANG HAIPING#]

Dear gromacs user：
 It seems ok now, I just used another tutorial as 
reference(http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B?highlight=replica).
  Thanks for all the help.
Best regards,
Haiping Zhang

发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 代表 HANNIBAL LECTER 

发送时间: 2014年5月22日 22:54
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] 答复: about exchange replica with replicas 140

Did you check the .err file as well? What does it say?

How many cores do each node in the HPC have? There might be some issues
with the supercomputer that you may be using? One of the nodes might have
some issues which is probably causing the problem?

I have used > 300 cores for replica exchange simulations without any issues.


On Thu, May 22, 2014 at 12:47 AM, #ZHANG HAIPING# wrote:

> Dear Justin:
> The scripts I used is as follow:
> ## Set job parameters
>
> ## Job Name
> #BSUB -J OpenMPI
>
> ## Queue  Name
> #BSUB -q medium_priority
>
> ## Output and Input Errors
> #BSUB -o job%J.out
> #BSUB -e job%J.err
>
> ## Specify walltime in HH:MM
> #BSUB -W 60:00
>
> ## 16 Processors per Host
> #BSUB -R "span[ptile=16]"
>
> ## Requesting for 32 cores
> #BSUB -n 140
>
> # Need to make our own machinefile
> MACHINEFILE=mymacs.$LSB_JOBID
> for i in `echo $LSB_HOSTS`
> do
> echo $i
> done > $MACHINEFILE
>
>
> ## load module enviroement
> module load openmpi-1.6.5-intel-v12.1.5
> module load intel-12.1.5
>
> ## Run mpi program
> cd /gpfs/home/hzhang020/REMD/remdrun/scratch
> /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core
> --report-bindings  -np 140 -machinefile $MACHINEFILE
> /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s
> prefix_.tpr -multi 140   -replex 3000
>
>
> There was not obvious error information, just have the output file size is
> always 0. After long time, I kill it myself.
>
>
> NOTE: The load imbalance in PME FFT and solve is 384%.
>   For optimal PME load balancing
>   PME grid_x (1728) and grid_y (1728) should be divisible by
> #PME_nodes_x (2)
>   and PME grid_y (1728) and grid_z (1728) should be divisible by
> #PME_nodes_y (1)
>
>
> NOTE: The load imbalance in PME FFT and solve is 384%.
>   For optimal PME load balancing
>   PME grid_x (1728) and grid_y (1728) should be divisible by
> #PME_nodes_x (2)
>   and PME grid_y (1728) and grid_z (1728) should be divisible by
> #PME_nodes_y (1)
>
> --
> WARNING: A process refused to die!
>
> Host: comp094
> PID:  6751
>
> This process may still be running and/or consuming resources.
>
> --
> --
> mpirun noticed that process rank 273 with PID 30914 on node comp122 exited
> on signal 9 (Killed).
> --
>
>
>
>
> 
> 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> 代表 Justin Lemkul <
> jalem...@vt.edu>
> 发送时间: 2014年5月22日 10:57
> 收件人: gmx-us...@gromacs.org
> 主题: Re: [gmx-users] about  exchange replica with  replicas 140
>
> On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote:
> > Dear gromacs user:
> >
> > I have encounter a problem when used HPC(high performance computer) to
> run replica exchange. I find that when I used replica over 128, it will not
> work, while under 128 , it is ok, even when I used cores much more than
> 128(several cores for one replica). The version  I used is
> gromacs-4.6.2-double-intel. Hope for you help.
> >
>
> You need to provide more information.  Specifically, what commands are you
> issuing?  What does "will not work" mean?  Is there a specific error you
> are
> getting?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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!
>
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>
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Re: [gmx-users] Gromacs for reverse transformation

[Tsjerk Wassenaar]

Hi Chandan,

You may have to write a mapping file, as explained in one of the tutorials
in the supplementary information of the paper. If that poses problems, you
can contact me. I may be interested in adding new mappings :)

Cheers,

Tsjerk
On May 22, 2014 6:42 PM, "Chandan Choudhury"  wrote:

> Hi Tsjerk,
> Do the scripts available in the backward.zip file
> http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help
> me to backmap a coarse-grained polymer?
>
> Chandan
>
>
> On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi sxn,
> >
> > I would argue that that method for reverse transformation is largely
> > obsolete. Please have a look at
> > http://www.cgmartini.nl/cgmartini/index.php/back
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> > wrote:
> >
> > > Hello,
> > >
> > > I want to do a reverse transformation of my system containing:
> bi-layer,
> > > protein and water.
> > >
> > > The Martini website (
> > > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says
> > to
> > > install gromacs version 3.3.1
> > >
> > > I am currently using 4.6.1 gromacs version.
> > >
> > > ques A: Is this version incapable of the transformation?
> > >
> > > Also, the martini website says to:
> > >
> > > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
> > > contains all necessary gromacs files for this exercise.*
> > >
> > > *2. Compile and/or source the modifi ed version of gromacs (remember
> this
> > > tool is based upon gromacs version 3.3.1 and needs the corresponding
> > tricks
> > > and threats to be compiled.)*
> > >
> > > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> > >
> > >
> > > ques B:On performing untar on rev_trans.tar.gz there is no
> > MARTINITUTORIAL
> > > directory
> > > ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
> > >
> > > KIndly help.
> > >
> > > Thanks,
> > > sxn
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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.
> >
>
>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gromacs for reverse transformation

[shivangi nangia]

Thanks a lot Tsjerk.


Thanks,
Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Thu, May 22, 2014 at 11:01 AM, Tsjerk Wassenaar wrote:

> Hi sxn,
>
> I would argue that that method for reverse transformation is largely
> obsolete. Please have a look at
> http://www.cgmartini.nl/cgmartini/index.php/back
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> wrote:
>
> > Hello,
> >
> > I want to do a reverse transformation of my system containing: bi-layer,
> > protein and water.
> >
> > The Martini website (
> > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says
> to
> > install gromacs version 3.3.1
> >
> > I am currently using 4.6.1 gromacs version.
> >
> > ques A: Is this version incapable of the transformation?
> >
> > Also, the martini website says to:
> >
> > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that
> > contains all necessary gromacs files for this exercise.*
> >
> > *2. Compile and/or source the modifi ed version of gromacs (remember this
> > tool is based upon gromacs version 3.3.1 and needs the corresponding
> tricks
> > and threats to be compiled.)*
> >
> > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> >
> >
> > ques B:On performing untar on rev_trans.tar.gz there is no
> MARTINITUTORIAL
> > directory
> > ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
> >
> > KIndly help.
> >
> > Thanks,
> > sxn
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning

[Szilárd Páll]

Two questions:
- Is the software configuration on these node identical, that is is
the compiler, MPI, CUDA, IB drivers, etc the same on the C2050 and K20
nodes?
- Are you using CUDA-aware MPI? (Have you tried different MPI installs?)

If the answer is yes & yes, than I suspect this could be related to
the MPI runtime doing something funky (and specific to the Fermi
hardware). Perhaps it's related to either:
- thread affinity: I've heard of instances when the IB driver set the
affinity and this clashed with mdrun's eager thread-affinity setting
behavior;
- GPU compute mode: I forgot already the order of things in the
detection/initialization (even though I wrote most/some of it), but
AFAR mdrun does GPU detection before it initialized MPI; this could
cause issues e.g. if the GPUs are in thread-exclusive mode, the MPI
launcher know that GPUs will be involved in the run, mdrun starts and
grabs the GPUs early during initialization, then the MPI stack (or IB
driver?) is unable to access the GPU afterwards.

To verify the former, try the "-pin off" mdrun option; for the latter
check the compute mode (use nvidia-smi) and if it is no default=0, set
it to this value -- if there is a job scheduler involved you may have
to change its settings or just an interactive session.


Cheers,
--
Szilárd


On Thu, May 22, 2014 at 5:31 PM, Thomas C. O'Connor  wrote:
> Hey,
>
> Yes, everything runs fine if I work on one node with one or more GPU's. The
> crash occurs, similar to the previous mailing list post:
>
> http://comments.gmane.org/gmane.science.biology.gromacs.user/63911
>
> It crashes when we attempt to work across multiple GPU enabled nodes. This
> happens when our cluster of C2050's is used but not when our nodes with
> K20's are used. The CPU architecture on the two node types are also
> slightly different but both are Intel hardware.
>
> Hopefully there is a solution.
>
> Thanks for the tips on launch configurations. I think my simulations are
> scaling pretty well with the GPU's.  I'm working with a dense city of many
> millions of atoms.
>
>
> On Wed, May 21, 2014 at 8:52 PM, Szilárd Páll wrote:
>
>> Hi,
>>
>> Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a
>> single GPU? How about two?
>>
>> Btw, unless you have some rather exotic setup, you won't be able to
>> get much improvement from using more than three, at most four GPUs per
>> node - you need CPU cores to match them (and a large system to deed
>> the GPUs and scale). Multi runs could work well, though.
>>
>> Cheers,
>>
>>
>> --
>> Szilárd
>>
>>
>> On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor 
>> wrote:
>> > Hey Folks,
>> >
>> > I'm attempting to run simulations on a multi-node gpu cluster and my
>> > simulations are crashing after flagging a open-mpi fork() warning:
>> >
>> >
>> *--*
>> > *An MPI process has executed an operation involving a call to the*
>> > *"fork()" system call to create a child process.  Open MPI is currently*
>> > *operating in a condition that could result in memory corruption or*
>> > *other system errors; your MPI job may hang, crash, or produce silent*
>> > *data corruption.  The use of fork() (or system() or other calls that*
>> > *create child processes) is strongly discouraged.*
>> >
>> > *The process that invoked fork was:*
>> >
>> > *  Local host:  lngpu019 (PID 11549)*
>> > *  MPI_COMM_WORLD rank: 18*
>> >
>> > *If you are *absolutely sure* that your application will successfully*
>> > *and correctly survive a call to fork(), you may disable this warning*
>> > *by setting the mpi_warn_on_fork MCA parameter to 0.*
>> >
>> *--*
>> >
>> >
>> > I saw a similar mailing-list post about this sort of issue from September
>> > 2013, but the thread had no resolution.
>> >
>> >
>> >- Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla
>> >C2050 GPU's.
>> >
>> >
>> >- we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi
>> >
>> >
>> >- I compiled GROMACS on one of the compute nodes with the C2050's.
>> >
>> > We also have a few nodes with newer K20 NVIDIA GPU's. When we compile
>> > GROMACS on these nodes we can run the code across multiple nodes and
>> GPU's
>> > without any errors.
>> >
>> > I don't know if the fork() error is directly related to the crash or not;
>> > or if there might be obscure, device specific object files outside my
>> build
>> > directory, that I should delete. Any insight you folks could provide to
>> > help me solve this issue would be appreciated.
>> >
>> > Thanks,
>> >
>> >
>> > --
>> > Thomas O'Connor
>> > Graduate Research Assistant
>> > MCS IGERT Fellow
>> >
>> > Department of Physics & Astronomy
>> > The Johns Hopkins University
>> > 3701 San Martin Drive
>> > Baltimore, MD 21218*tocon...@jhu.edu *410.516.8587
>> > --
>> > Gromacs Users mailing list
>> >
>> > 

Re: [gmx-users] Gromacs for reverse transformation

[shivangi nangia]

Hello Tsjerk,

Is there any example/tutorial on how to use the backward apart from the
notes in the initram.sh

Thanks,
sxn




On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar  wrote:

> Hi Chandan,
>
> You may have to write a mapping file, as explained in one of the tutorials
> in the supplementary information of the paper. If that poses problems, you
> can contact me. I may be interested in adding new mappings :)
>
> Cheers,
>
> Tsjerk
> On May 22, 2014 6:42 PM, "Chandan Choudhury"  wrote:
>
> > Hi Tsjerk,
> > Do the scripts available in the backward.zip file
> > http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp
> > me to backmap a coarse-grained polymer?
> >
> > Chandan
> >
> >
> > On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar 
> > wrote:
> >
> > > Hi sxn,
> > >
> > > I would argue that that method for reverse transformation is largely
> > > obsolete. Please have a look at
> > > http://www.cgmartini.nl/cgmartini/index.php/back
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > >
> > > On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > I want to do a reverse transformation of my system containing:
> > bi-layer,
> > > > protein and water.
> > > >
> > > > The Martini website (
> > > > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation)
> says
> > > to
> > > > install gromacs version 3.3.1
> > > >
> > > > I am currently using 4.6.1 gromacs version.
> > > >
> > > > ques A: Is this version incapable of the transformation?
> > > >
> > > > Also, the martini website says to:
> > > >
> > > > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory
> that
> > > > contains all necessary gromacs files for this exercise.*
> > > >
> > > > *2. Compile and/or source the modifi ed version of gromacs (remember
> > this
> > > > tool is based upon gromacs version 3.3.1 and needs the corresponding
> > > tricks
> > > > and threats to be compiled.)*
> > > >
> > > > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> > > >
> > > >
> > > > ques B:On performing untar on rev_trans.tar.gz there is no
> > > MARTINITUTORIAL
> > > > directory
> > > > ques C: On performing untar on gmx_rev.tar.gz there is no bin folder
> > > >
> > > > KIndly help.
> > > >
> > > > Thanks,
> > > > sxn
> > > > --
> > > > 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-usersor
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> >
> > --
> > Chandan Kumar Choudhury
> > National Chemical Laboratory, Pune
> > 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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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[gmx-users] Odd protein behavior in MD

[Steve Seibold]

I ran a 8 ns simulation on a small protein in a water box using PBC. I then 
calculated the RMS using g_rms command. When I plotted the outcome my rms graph 
looked like a Histogram instead of a rms plot. I then took a region of the 
trajectories and view them in VMD. The protein starts out ok, but suddenly 
blows up in the since that separate parts of the protein went to the four 
corners of the box...I thought maybe this was a problem of PBC where parts of 
my protein were leaving the box and so, I attempted to center protein and water 
back into the center of the box using the following procedure:

trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc

However, this did not correct the problem...Can someone please inform as to 
what the problem is??? The total energy and potential energy looks ok and so, I 
am lost as to what is happening or how to fix it.


Thanks, Steve
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Re: [gmx-users] Gromacs for reverse transformation

[Tsjerk Wassenaar]

Hi sxn,

The paper describing the method has a tutorial as supplementary material.
It's also available from our site at the University of Erlangen, but I'l
have to look up the address. In addition, Alex de Vries from Groningen
recently developed another tutorial for a hands-on session he arranged. Not
sure if it is available online, I'll ask him to seenif we can add it to the
backward site at cgmartini.nl.

Cheers,

Tsjerk
On May 22, 2014 9:28 PM, "shivangi nangia" 
wrote:

> Hello Tsjerk,
>
> Is there any example/tutorial on how to use the backward apart from the
> notes in the initram.sh
>
> Thanks,
> sxn
>
>
>
>
> On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hi Chandan,
> >
> > You may have to write a mapping file, as explained in one of the
> tutorials
> > in the supplementary information of the paper. If that poses problems,
> you
> > can contact me. I may be interested in adding new mappings :)
> >
> > Cheers,
> >
> > Tsjerk
> > On May 22, 2014 6:42 PM, "Chandan Choudhury"  wrote:
> >
> > > Hi Tsjerk,
> > > Do the scripts available in the backward.zip file
> > >
> http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp
> > > me to backmap a coarse-grained polymer?
> > >
> > > Chandan
> > >
> > >
> > > On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar 
> > > wrote:
> > >
> > > > Hi sxn,
> > > >
> > > > I would argue that that method for reverse transformation is largely
> > > > obsolete. Please have a look at
> > > > http://www.cgmartini.nl/cgmartini/index.php/back
> > > >
> > > > Cheers,
> > > >
> > > > Tsjerk
> > > >
> > > >
> > > > On Thu, May 22, 2014 at 4:26 PM, shivangi nangia
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I want to do a reverse transformation of my system containing:
> > > bi-layer,
> > > > > protein and water.
> > > > >
> > > > > The Martini website (
> > > > > http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation)
> > says
> > > > to
> > > > > install gromacs version 3.3.1
> > > > >
> > > > > I am currently using 4.6.1 gromacs version.
> > > > >
> > > > > ques A: Is this version incapable of the transformation?
> > > > >
> > > > > Also, the martini website says to:
> > > > >
> > > > > *"1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory
> > that
> > > > > contains all necessary gromacs files for this exercise.*
> > > > >
> > > > > *2. Compile and/or source the modifi ed version of gromacs
> (remember
> > > this
> > > > > tool is based upon gromacs version 3.3.1 and needs the
> corresponding
> > > > tricks
> > > > > and threats to be compiled.)*
> > > > >
> > > > > *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC"*
> > > > >
> > > > >
> > > > > ques B:On performing untar on rev_trans.tar.gz there is no
> > > > MARTINITUTORIAL
> > > > > directory
> > > > > ques C: On performing untar on gmx_rev.tar.gz there is no bin
> folder
> > > > >
> > > > > KIndly help.
> > > > >
> > > > > Thanks,
> > > > > sxn
> > > > > --
> > > > > 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-usersor
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Tsjerk A. Wassenaar, Ph.D.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
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> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > >
> > > --
> > > Chandan Kumar Choudhury
> > > National Chemical Laboratory, Pune
> > > India
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> > --
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> >
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> >
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>
> * Please search the archive

Re: [gmx-users] Odd protein behavior in MD

[Mark Abraham]

Hi,

The usual workflow to fix these kinds of pbc issues can be found here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark


On Thu, May 22, 2014 at 9:48 PM, Steve Seibold  wrote:

> I ran a 8 ns simulation on a small protein in a water box using PBC. I
> then calculated the RMS using g_rms command. When I plotted the outcome my
> rms graph looked like a Histogram instead of a rms plot. I then took a
> region of the trajectories and view them in VMD. The protein starts out ok,
> but suddenly blows up in the since that separate parts of the protein went
> to the four corners of the box...I thought maybe this was a problem of PBC
> where parts of my protein were leaving the box and so, I attempted to
> center protein and water back into the center of the box using the
> following procedure:
>
> trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc
>
> However, this did not correct the problem...Can someone please inform as
> to what the problem is??? The total energy and potential energy looks ok
> and so, I am lost as to what is happening or how to fix it.
>
>
> Thanks, Steve
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] g_disre problem

[B Harish]

I'm trying to use g_disre to analyze NOE-derived distance restraints in my 
simulation as :
g_disre -s gromacs46-run20.tpr -f run-20-dt100-nojump.pdb
And I get the error (logfile attached) :
Program g_disre, VERSION 4.6.5
Source code file: /root/gromacs-4.6.5/src/tools/gmx_disre.c, line: 189

Fatal error:
tpr inconsistency. ndr = 728, label = 0

Now there are 728 distance restraints, indexed from 0 to 727 in the itp file 
and they are read correctly (from log file: There are 4646 distance restraints 
involving 4646 atom pairs, there is more than one pair in each restraint).
So I don’t know how to fix this now.
Thanks in advance for any help,
Harish




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[gmx-users] from amber to opls

[Rebeca García Fandiño]

Hi,
I have done a simulation of an organic molecule (a cyclodextrin) using 
GAFF/AMBER parameters, and I would like to compare the results using another 
force-field (OPLS or CHARMM). Is there any direct way to go from the topology 
for AMBER to the topology for OPLS or CHARMM?
Thanks a lot for your help in advance.
Best wishes,
Rebeca.

Dr. Rebeca Garcia
Santiago de Compostela University
Spain
  
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Re: [gmx-users] from amber to opls

[Justin Lemkul]

On 5/22/14, 5:19 PM, Rebeca García Fandiño wrote:

Hi,
I have done a simulation of an organic molecule (a cyclodextrin) using 
GAFF/AMBER parameters, and I would like to compare the results using another 
force-field (OPLS or CHARMM). Is there any direct way to go from the topology 
for AMBER to the topology for OPLS or CHARMM?


You can't simply translate one force field to another.  You need to derive a new 
topology that is consistent with the other force field.  For CHARMM, you can use 
the ParamChem server to derive parameters under CGenFF; the output topologies 
are generally very high quality, though some small empirical adjustments may be 
necessary, but the majority of the hard work is already done :)


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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[gmx-users] mdrun_mpi with cmake

[Soren Wacker]

Hi,

I would like to generate specifically mdrun with mpi support.

with configure/make it was possible to use

configure ...
make mdrun
make install mdrun

How would you do this with cmake?

best regards
Soren
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Re: [gmx-users] mdrun_mpi with cmake

[Szilárd Páll]

http://www.gromacs.org/Documentation/Installation_Instructions#4.2._Using_CMake_command-line_options

With 4.5/6 we generate a target with CMake called "install-mdrun", so
make install-mdrun
will work.

With 5.0 things will change a bit and you'll have to turn on an
"mdrun-only build".

--
Szilárd


On Fri, May 23, 2014 at 12:16 AM, Soren Wacker  wrote:
> Hi,
>
> I would like to generate specifically mdrun with mpi support.
>
> with configure/make it was possible to use
>
> configure ...
> make mdrun
> make install mdrun
>
> How would you do this with cmake?
>
> best regards
> Soren
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>
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Re: [gmx-users] mdrun_mpi with cmake

[Soren Wacker]

Thanks!

That means you compile everything with 

cmake 
make
#and only at the last step the build is limited to mdrun?
make-mdrun

Do you already know how you will turn on an 'mdrun-only build' ?

best
Soren
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Re: [gmx-users] mdrun_mpi with cmake

[Justin Lemkul]

On 5/22/14, 6:36 PM, Soren Wacker wrote:

Thanks!

That means you compile everything with

cmake 
make
#and only at the last step the build is limited to mdrun?
make-mdrun

Do you already know how you will turn on an 'mdrun-only build' ?



No, use cmake -DGMX_BUILD_MDRUN_ONLY=ON

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON

[Soren Wacker]

Ok, 

actually, both solutions generated mdrun_mpi.
Would you recommend to set a suffix for the libraries as well?

@Justin: I've got 
>  Manually-specified variables were not used by the project:
>
>GMX_BUILD_MDRUN_ONLY

Does this mean the variable is not used at all, or just not here? Or should I 
set it as environment variable???
Is this the solution for gromacs 5?
I am compiling 4.6.5.

cmake command was:
cmake .. -DFFTWF_INCLUDE_DIR=/home/swacker/Programme/fftw3/single/include 
-DFFTWF_LIBRARY=~/Programme/fftw3/single/lib/libfftw3f.a 
-DCMAKE_INSTALL_PREFIX=~/Programme/gromacs/gromacs-4.6.5-gcc-fftw3-single 
-DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_DEFAULT_SUFFIX=OFF 
-DGMX_BUILD_MDRUN_ONLY=ON




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, May 22, 2014 4:38 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdrun_mpi with cmake

On 5/22/14, 6:36 PM, Soren Wacker wrote:
> Thanks!
>
> That means you compile everything with
>
> cmake 
> make
> #and only at the last step the build is limited to mdrun?
> make-mdrun
>
> Do you already know how you will turn on an 'mdrun-only build' ?
>

No, use cmake -DGMX_BUILD_MDRUN_ONLY=ON

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON

[Justin Lemkul]

On 5/22/14, 6:57 PM, Soren Wacker wrote:

Ok,

actually, both solutions generated mdrun_mpi.
Would you recommend to set a suffix for the libraries as well?

@Justin: I've got

  Manually-specified variables were not used by the project:

GMX_BUILD_MDRUN_ONLY


Does this mean the variable is not used at all, or just not here? Or should I 
set it as environment variable???
Is this the solution for gromacs 5?


Yes, that is for 5.0.

-Justin


I am compiling 4.6.5.

cmake command was:
cmake .. -DFFTWF_INCLUDE_DIR=/home/swacker/Programme/fftw3/single/include 
-DFFTWF_LIBRARY=~/Programme/fftw3/single/lib/libfftw3f.a 
-DCMAKE_INSTALL_PREFIX=~/Programme/gromacs/gromacs-4.6.5-gcc-fftw3-single 
-DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_DEFAULT_SUFFIX=OFF 
-DGMX_BUILD_MDRUN_ONLY=ON




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, May 22, 2014 4:38 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdrun_mpi with cmake

On 5/22/14, 6:36 PM, Soren Wacker wrote:

Thanks!

That means you compile everything with

cmake 
make
#and only at the last step the build is limited to mdrun?
make-mdrun

Do you already know how you will turn on an 'mdrun-only build' ?



No, use cmake -DGMX_BUILD_MDRUN_ONLY=ON

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON

[Soren Wacker]

...and apparently everything gets compiled.
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Re: [gmx-users] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON

[Soren Wacker]

Thanks!
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[gmx-users] counter ions in coarse grained simulations

[Neha Gandhi]

Hi List,

My query is not really related to gromacs but I appreciate response from
people who might have tried using coarse grained simualtions using Martini
force field in gromacs.

I haven't come across tutorial or mailing list where people have added
counter ions to a coarse grained protein system. Do we also coarse grained
counter-ions ? or Do I assume that some sort of potential will take care of
the effect? Or are the parameters from atomistic force fields are retained
for counter-ions?

How do I add counter-ions in gromacs to coarse grained topology?

Your feedback is appreciated.

Regards,
Neha
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[gmx-users] rhombic dodecahedron construction

[Trayder Thomas]

Hi,

I'm trying to figure out how to construct a rhombic dodecahedron for a
membrane system.
The manual (Section 3.2.1) states:

"There are two different orientations of a rhombic dodecahedron that
satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the
orientation which has a square intersection with the xy-plane. This
orientation was chosen because the first two box vectors coincide with the
x and y-axis, which is easier to comprehend. The other orientation can be
useful for simulations of membrane proteins. In this case the cross-section
with the xy-plane is a hexagon, which has an area which is 14% smaller than
the area of a square with the same image distance. The height of the box
(cz) should be changed to obtain an optimal spacing."

I can't figure out how to construct the system with a hexagon on the x-y
plane, I presume I can rotate the box but I can only visualise the result
as a triclinic cell.
I also can't figure out how to adjust the height of the box, editconf only
accepts a single magnitude for dodecahedron vector lengths.

Any help would be greatly appreciated.
Thanks in advance,

-Trayder
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Re: [gmx-users] RDF of solvation shell molecules

[sujithkakkat .]

Hello Chandan,

 Thank you for the response.

  I have used g_rdf, but I guess it gives the RDF for the whole system.
Say, if I choose water oxygen, it will plot RDF from water molecules in the
whole system. But, I want the RDF for the solvation shell water molecules
,leaving the bulk water . I came across such a plot in an article where the
author studied the structure of solvation shell . So do you think it is
possible to do that GROMACS?


Regards,

Sujith.


On Thu, May 22, 2014 at 9:31 PM, Chandan Choudhury wrote:

> Hi Sujith,
>
> g_rdf is the tool you need.
>
> Chandan
>
>
> On Thu, May 22, 2014 at 8:18 PM, sujithkakkat .  >wrote:
>
> > Hello,
> >
> > I would like to know if it is possible to plot the RDF of water
> > molecules belonging to the solvation shell of a solute. I mean, I want to
> > know the effect of the solute on the water arrangement in the solvation
> > shell.  Is there a way to do this?
> >
> > Regards,
> >
> > Sujith.
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>
>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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