[gmx-users] mdrun_mpi issue for CHARMM36 FF

[Anirban]

Hi ALL,

I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
mpirun and gives proper output. But whenever I try to submit it on more
than 5 nodes, the job gets killed with the following error:

-

starting mdrun 'Protein'
5000 steps, 10.0 ps.

NOTE: Turning on dynamic load balancing

Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error

=
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 256
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=
[proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
[proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error
waiting for event
.
.
.
--

Why is this happening? Is it related to DD and PME? How to solve it? Any
suggestion is welcome.
Sorry for re-posting.


Thanks and regards,

Anirban
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Anirban]

On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh
wrote:

> Dear gmx users,
>
> Anybody can guide me to some articles which introduces CHARMM36
> forcefield? I want to study about this forcefield.
>
>
Have a look at this paper:

http://pubs.acs.org/doi/abs/10.1021/jp101759q

 -Anirban

Thanks in advance,
> Shima
>
>   --
> *From:* Anirban 
> *To:* Shima Arasteh ; Discussion list for
> GROMACS users 
> *Sent:* Friday, May 11, 2012 9:22 PM
>
> *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
> On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>  CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a
> good output of simulation.
> Before this, Justin also suggested me for CHARMM36. Ok, I will use
> CHARMM36. But about the atom types, it's not still clear for me what I need
> to do. If I use the CHARMM36, am I supposed to build berger lipids?
>
>
> Actually if you use CHARMM36 FF then no need to use Berger parameters,
> since CHARMM36 FF already have the all-atom POPC parameters. But there are
> differences among the atom types. So you can use these POPC files (Peter
> Lai provided me these files and these were generated for the following
> work: (please reference):
> Lai, P.C. and Crasto, C.J.
> Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
> Front. Gene.
> Volume 3 Year 2012 Number 61
> DOI: 10.3389/fgene.2012.00061)
>
> These files worked fine for me (with grompp). Include the popc.itp file in
> your .top file.
>
> -Anirban
>
>
>  Thanks,
> Shima
>
>   --
> *From:* Anirban 
> *To:* Shima Arasteh 
> *Sent:* Friday, May 11, 2012 8:58 PM
>
> *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
> On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>  Dear Anirban,
> No, I have not done. Because I didn't know I need Berger lipids for this
> simulation.
>
>
> Actually I think the coordinate and topology files from Tieleman's site
> are in accordance with the Berger lipid parameters and hence works with the
> united-atom gromos FF. You can also get CHARMM27 lipids from
> http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the
> atom-type errors can be solved if you can build a proper .hdb file with the
> proper corrections for the violating atom names.
>
> -Anirban
>
>
>  Thanks for you reply,
> Cheers,
> Shima
>
>--
> *From:* Anirban 
> *To:* Shima Arasteh ; Discussion list for
> GROMACS users 
> *Sent:* Friday, May 11, 2012 8:10 PM
> *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
> On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>  Dear gmx users,
>
> I'm going to simulate the POPC in water.
> I downloaded required files in Tielman site and made the .top file. Then
> included the CHARMM27.ff in the .top file.
> When I run the grompp I get the fatal error as below:
> Atomtype CB not found
>
> I have done the same with gromos87.ff . But I didn't see any error.
> What's the problem?
> Anybody may suggest me how to solve this problem? Is this because of the
> forcefield? Or something in .top file goes wrong?
>
>
> Have properly edited the CHARMM27 bonded and nonbonded .itp files to
> include the Berger lipid parameters and have you included the POPC
> topology? You can follow this tutorial to get an idea:
>
> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
> -Anirban
>
>
>   Thanks,
> Shima
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
>
>
>
>
>
>
>
>
>
>
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Jesper Sørensen]

I would say looking at the CHARMM force field website would be the first thing 
to do. Google: CHARMM FORCE FIELD, and you should get the relevant pages... The 
articles are listed on the website...

/Jesper


On May 11, 2012, at 9:19 PM, Shima Arasteh wrote:

> Dear gmx users,
> 
> Anybody can guide me to some articles which introduces CHARMM36  forcefield? 
> I want to study about this forcefield.
> 
> Thanks in advance,
> Shima
> 
> From: Anirban 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users  
> Sent: Friday, May 11, 2012 9:22 PM
> Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
> 
> 
> 
> On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh  
> wrote:
> CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good 
> output of simulation.
> Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. 
> But about the atom types, it's not still clear for me what I need to do. If I 
> use the CHARMM36, am I supposed to build berger lipids?
> 
>  
> Actually if you use CHARMM36 FF then no need to use Berger parameters, since 
> CHARMM36 FF already have the all-atom POPC parameters. But there are 
> differences among the atom types. So you can use these POPC files (Peter Lai 
> provided me these files and these were generated for the following work: 
> (please reference):
> Lai, P.C. and Crasto, C.J.
> Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
> Front. Gene.
> Volume 3 Year 2012 Number 61
> DOI: 10.3389/fgene.2012.00061)
>  
> These files worked fine for me (with grompp). Include the popc.itp file in 
> your .top file.
>  
> -Anirban
>  
> Thanks,
> Shima
> 
> From: Anirban 
> To: Shima Arasteh  
> Sent: Friday, May 11, 2012 8:58 PM
> 
> Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
> 
> 
> 
> On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh  
> wrote:
> Dear Anirban,
> No, I have not done. Because I didn't know I need Berger lipids for this 
> simulation. 
>  
> Actually I think the coordinate and topology files from Tieleman's site are 
> in accordance with the Berger lipid parameters and hence works with the 
> united-atom gromos FF. You can also get CHARMM27 lipids from 
> http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the 
> atom-type errors can be solved if you can build a proper .hdb file with the 
> proper corrections for the violating atom names.
>  
> -Anirban
>  
> Thanks for you reply,
> Cheers,
> Shima
> 
> From: Anirban 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users  
> Sent: Friday, May 11, 2012 8:10 PM
> Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
> 
> 
> 
> On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
> wrote:
> Dear gmx users,
> 
> I'm going to simulate the POPC in water.
> I downloaded required files in Tielman site and made the .top file. Then 
> included the CHARMM27.ff in the .top file.
> When I run the grompp I get the fatal error as below:
> Atomtype CB not found
> 
> I have done the same with gromos87.ff . But I didn't see any error.
> What's the problem?
> Anybody may suggest me how to solve this problem? Is this because of the 
> forcefield? Or something in .top file goes wrong?
> 
> 
> Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
> the Berger lipid parameters and have you included the POPC topology? You can 
> follow this tutorial to get an idea:
> 
> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
> 
> -Anirban
>  
> Thanks,
> Shima
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

Dear gmx users,

Anybody can guide me to some articles which introduces CHARMM36  forcefield? I 
want to study about this forcefield.

Thanks in advance,
Shima




 From: Anirban 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, May 11, 2012 9:22 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh  
wrote:

CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good 
output of simulation.
>Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. 
>But about the atom types, it's not still clear for me what I need to do. If I 
>use the CHARMM36, am I supposed to build berger lipids?
>
>
 
Actually if you use CHARMM36 FF then no need to use Berger parameters, since 
CHARMM36 FF already have the all-atom POPC parameters. But there are 
differences among the atom types. So you can use these POPC files (Peter Lai 
provided me these files and these were generated for the following work: 
(please reference):
Lai, P.C. and Crasto, C.J.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061) 
 
These files worked fine for me (with grompp). Include the popc.itp file in your 
.top file.
 
-Anirban
 
Thanks,
>Shima
>
>
>
>
>
> From: Anirban 
>To: Shima Arasteh  
>Sent: Friday, May 11, 2012 8:58 PM 
>
>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
>
>
>
>On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh  
>wrote:
>
>Dear Anirban,
>>No, I have not done. Because I didn't know I need Berger lipids for this 
>>simulation. 
>>
> 
>Actually I think the coordinate and topology files from Tieleman's site are in 
>accordance with the Berger lipid parameters and hence works with the 
>united-atom gromos FF. You can also get CHARMM27 lipids from 
>http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the 
>atom-type errors can be solved if you can build a proper .hdb file with the 
>proper corrections for the violating atom names.
> 
>-Anirban
> 
>Thanks for you reply,
>>Cheers,
>>Shima
>>
>>
>>
>>
>>
>> From: Anirban 
>>To: Shima Arasteh ; Discussion list for GROMACS 
>>users  
>>Sent: Friday, May 11, 2012 8:10 PM
>>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>>
>>
>>
>>
>>
>>
>>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
>>wrote:
>>
>>Dear gmx users,
>>>
>>>
>>>I'm going to simulate the POPC in water.
>>>I downloaded required files in Tielman site and made the .top file. Then 
>>>included the CHARMM27.ff in the .top file.
>>>When I run the grompp I get the fatal error as below:
>>>Atomtype CB not found
>>>
>>>
>>>
>>>I have done the same with gromos87.ff . But I didn't see any error.
>>>What's the problem?
>>>Anybody may suggest me how to solve this problem? Is this because of the 
>>>forcefield? Or something in .top file goes wrong?
>>>
>>>
>>
>>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
>>the Berger lipid parameters and have you included the POPC topology? You can 
>>follow this tutorial to get an idea:
>>
>>https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>>
>>-Anirban
>> 
>>Thanks,
>>>Shima
>>>
>>>--
>>>gmx-users mailing list    gmx-users@gromacs.org
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at 
>>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-requ...@gromacs.org.
>>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
>
>-- 
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Re: [gmx-users] editconf and g_editconf confusion

[Nitin Agrawal]

Thank you for your clarification.

On Sat, May 12, 2012 at 2:51 AM, Justin A. Lemkul  wrote:

>
>
> On 5/11/12 7:40 PM, Nitin Agrawal wrote:
>
>> Hi,
>>
>> Can anyone please tell me what is the difference between the commands
>> editconf
>> and g_editconf? If there is no difference then why do some systems
>> recognize
>> g_editconf but not editconf?
>>
>>
> There is no difference.  g_editconf is just editconf but with a prefix.
>  Some Linux distributions (like Fedora) have Gromacs packages that have
> such nomenclature.  I believe the reason this was done was to avoid
> potential conflicts between the names of certain tools and other programs
> that may be installed on the system.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Regards,
Nitin Agrawal,
Master's Student (Bioinformatics)
University of Turku,Finland
B.Tech (Biotechnology)
National Institute of Technology,Durgapur,India
Blog:http://notjustanyotherblog.blogspot.com/
-- 
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Re: [gmx-users] editconf and g_editconf confusion

[Justin A. Lemkul]

On 5/11/12 7:40 PM, Nitin Agrawal wrote:

Hi,

Can anyone please tell me what is the difference between the commands editconf
and g_editconf? If there is no difference then why do some systems recognize
g_editconf but not editconf?



There is no difference.  g_editconf is just editconf but with a prefix.  Some 
Linux distributions (like Fedora) have Gromacs packages that have such 
nomenclature.  I believe the reason this was done was to avoid potential 
conflicts between the names of certain tools and other programs that may be 
installed on the system.


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] editconf and g_editconf confusion

[Nitin Agrawal]

Hi,

Can anyone please tell me what is the difference between the commands
editconf and g_editconf? If there is no difference then why do some systems
recognize g_editconf but not editconf?

-- 
Regards,
Nitin Agrawal,
Master's Student (Bioinformatics)
University of Turku,Finland
B.Tech (Biotechnology)
National Institute of Technology,Durgapur,India
Blog:http://notjustanyotherblog.blogspot.com/
-- 
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[gmx-users] Number of native contacts rho

[Sanku M]

Hi,
  Is there any tool in gromacs that can compute the fraction of native contacts 
 "rho" ( i,e  the typical parameter that quantifies how close the folding 
protein is to the native ) ?
Thanks
Sanku-- 
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Re: [gmx-users] General amber force field in GROMACS

[Justin A. Lemkul]

On 5/11/12 3:54 PM, Milinda Samaraweera wrote:


Hi Guys

Could some one please let me know how to convert general amber force field bond
force constents to GROMACS bong function 1 type.



Bond type 1 is a simple harmonic bond.  You need an equilibrium length and force 
constant in appropriate units, per Table 5.5 of the manual.  Likely a simple 
unit conversion is all that is necessary, depending on the source of your 
parameters.


-Justin

--


Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] General amber force field in GROMACS

[Milinda Samaraweera]

 Hi Guys

Could some one please let me know how to convert general amber force field bond 
force constents to GROMACS bong function 1 type.

Thanks so much


Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA-- 
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Re: [gmx-users] movement in 2 directions - remove one degree of freedom

[Oliver Stueker]

Hi,

as an alternative of applying position restraints to only the y-component,
one can also define a freeze-group only to act on the Y-axis by using:

freezedim N Y N

see: http://manual.gromacs.org/online/mdp_opt.html#neq  freezegrps and freezedim

Oliver

On Fri, May 11, 2012 at 7:39 AM, Erik Marklund  wrote:
>
> 11 maj 2012 kl. 14.38 skrev Steven Neumann:
>
> Dear Gromacs Users,
>
> Is there any way in Gromacs which will allow me to contraint some of the
> atoms in the system to move only in the coordinate X and Z? I do not want
> some of my atoms to move in Y direction. Do you know how to do this?
>
>
> Hi,
>
> Not exactly. But you can apply position restraints with zero force constants
>  in X and Z directions. This will allow some movement in the Y direction,
> but the extent depends on your force constant in the Y direction.
>
> Erik
>
> Steven
> --
> gmx-users mailing list    gmx-users@gromacs.org
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>
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

OK, I'll give it a try.
Thank you again! :-)

Cheers,
Shima




 From: Anirban 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, May 11, 2012 9:22 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh  
wrote:

CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good 
output of simulation.
>Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. 
>But about the atom types, it's not still clear for me what I need to do. If I 
>use the CHARMM36, am I supposed to build berger lipids?
>
>
 
Actually if you use CHARMM36 FF then no need to use Berger parameters, since 
CHARMM36 FF already have the all-atom POPC parameters. But there are 
differences among the atom types. So you can use these POPC files (Peter Lai 
provided me these files and these were generated for the following work: 
(please reference):
Lai, P.C. and Crasto, C.J.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061) 
 
These files worked fine for me (with grompp). Include the popc.itp file in your 
.top file.
 
-Anirban
 
Thanks,
>Shima
>
>
>
>
>
> From: Anirban 
>To: Shima Arasteh  
>Sent: Friday, May 11, 2012 8:58 PM 
>
>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
>
>
>
>On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh  
>wrote:
>
>Dear Anirban,
>>No, I have not done. Because I didn't know I need Berger lipids for this 
>>simulation. 
>>
> 
>Actually I think the coordinate and topology files from Tieleman's site are in 
>accordance with the Berger lipid parameters and hence works with the 
>united-atom gromos FF. You can also get CHARMM27 lipids from 
>http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the 
>atom-type errors can be solved if you can build a proper .hdb file with the 
>proper corrections for the violating atom names.
> 
>-Anirban
> 
>Thanks for you reply,
>>Cheers,
>>Shima
>>
>>
>>
>>
>>
>> From: Anirban 
>>To: Shima Arasteh ; Discussion list for GROMACS 
>>users  
>>Sent: Friday, May 11, 2012 8:10 PM
>>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>>
>>
>>
>>
>>
>>
>>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
>>wrote:
>>
>>Dear gmx users,
>>>
>>>
>>>I'm going to simulate the POPC in water.
>>>I downloaded required files in Tielman site and made the .top file. Then 
>>>included the CHARMM27.ff in the .top file.
>>>When I run the grompp I get the fatal error as below:
>>>Atomtype CB not found
>>>
>>>
>>>
>>>I have done the same with gromos87.ff . But I didn't see any error.
>>>What's the problem?
>>>Anybody may suggest me how to solve this problem? Is this because of the 
>>>forcefield? Or something in .top file goes wrong?
>>>
>>>
>>
>>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
>>the Berger lipid parameters and have you included the POPC topology? You can 
>>follow this tutorial to get an idea:
>>
>>https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>>
>>-Anirban
>> 
>>Thanks,
>>>Shima
>>>
>>>--
>>>gmx-users mailing list    gmx-users@gromacs.org
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at 
>>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-requ...@gromacs.org.
>>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>
>
>-- 
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Anirban]

On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh  wrote:

>  CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a
> good output of simulation.
> Before this, Justin also suggested me for CHARMM36. Ok, I will use
> CHARMM36. But about the atom types, it's not still clear for me what I need
> to do. If I use the CHARMM36, am I supposed to build berger lipids?
>
>
Actually if you use CHARMM36 FF then no need to use Berger parameters,
since CHARMM36 FF already have the all-atom POPC parameters. But there are
differences among the atom types. So you can use these POPC files (Peter
Lai provided me these files and these were generated for the following
work: (please reference):
Lai, P.C. and Crasto, C.J.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061)

These files worked fine for me (with grompp). Include the popc.itp file in
your .top file.

-Anirban


>  Thanks,
> Shima
>
>   --
> *From:* Anirban 
> *To:* Shima Arasteh 
> *Sent:* Friday, May 11, 2012 8:58 PM
>
> *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
> On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>  Dear Anirban,
> No, I have not done. Because I didn't know I need Berger lipids for this
> simulation.
>
>
> Actually I think the coordinate and topology files from Tieleman's site
> are in accordance with the Berger lipid parameters and hence works with the
> united-atom gromos FF. You can also get CHARMM27 lipids from
> http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the
> atom-type errors can be solved if you can build a proper .hdb file with the
> proper corrections for the violating atom names.
>
> -Anirban
>
>
>  Thanks for you reply,
> Cheers,
> Shima
>
>--
> *From:* Anirban 
> *To:* Shima Arasteh ; Discussion list for
> GROMACS users 
> *Sent:* Friday, May 11, 2012 8:10 PM
> *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
> On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>  Dear gmx users,
>
> I'm going to simulate the POPC in water.
> I downloaded required files in Tielman site and made the .top file. Then
> included the CHARMM27.ff in the .top file.
> When I run the grompp I get the fatal error as below:
> Atomtype CB not found
>
> I have done the same with gromos87.ff . But I didn't see any error.
> What's the problem?
> Anybody may suggest me how to solve this problem? Is this because of the
> forcefield? Or something in .top file goes wrong?
>
>
> Have properly edited the CHARMM27 bonded and nonbonded .itp files to
> include the Berger lipid parameters and have you included the POPC
> topology? You can follow this tutorial to get an idea:
>
> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
> -Anirban
>
>
>   Thanks,
> Shima
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
>
>
>
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good 
output of simulation.
Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36. 
But about the atom types, it's not still clear for me what I need to do. If I 
use the CHARMM36, am I supposed to build berger lipids?

Thanks,
Shima




 From: Anirban 
To: Shima Arasteh  
Sent: Friday, May 11, 2012 8:58 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh  
wrote:

Dear Anirban,
>No, I have not done. Because I didn't know I need Berger lipids for this 
>simulation. 
>
 
Actually I think the coordinate and topology files from Tieleman's site are in 
accordance with the Berger lipid parameters and hence works with the 
united-atom gromos FF. You can also get CHARMM27 lipids from 
http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the 
atom-type errors can be solved if you can build a proper .hdb file with the 
proper corrections for the violating atom names.
 
-Anirban
 
Thanks for you reply,
>Cheers,
>Shima
>
>
>
>
>
> From: Anirban 
>To: Shima Arasteh ; Discussion list for GROMACS 
>users  
>Sent: Friday, May 11, 2012 8:10 PM
>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
>
>
>
>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
>wrote:
>
>Dear gmx users,
>>
>>
>>I'm going to simulate the POPC in water.
>>I downloaded required files in Tielman site and made the .top file. Then 
>>included the CHARMM27.ff in the .top file.
>>When I run the grompp I get the fatal error as below:
>>Atomtype CB not found
>>
>>
>>
>>I have done the same with gromos87.ff . But I didn't see any error.
>>What's the problem?
>>Anybody may suggest me how to solve this problem? Is this because of the 
>>forcefield? Or something in .top file goes wrong?
>>
>>
>
>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
>the Berger lipid parameters and have you included the POPC topology? You can 
>follow this tutorial to get an idea:
>
>https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
>-Anirban
> 
>Thanks,
>>Shima
>>
>>--
>>gmx-users mailing list    gmx-users@gromacs.org
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at 
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org.
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>-- 
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[gmx-users] g_mdmat

[francesca vitalini]

Dear Gromacs user,
I'm trying to calculate de distances between residues in a trajectory with
g_mdmat and I'm coming across a problem while trying to restrict only to a
smaller number of residues providing an index file. in fact what I get is a
matrix as big as if I use all the residues, and the area of interest is
plotted through xpm2eps only in the lower left corner. How can I manage to
obtain a plot that only focuses on the residues provided by the index file?
I have been searching the mailing list but couldn't find an answer to that.
Thank you in advance.
Best

-- 
Francesca Vitalini
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Re: [gmx-users] Create Bond between new residues

[Steven Neumann]

Well, impressive explanation! Thank you very much!

Steven

On Fri, May 11, 2012 at 4:38 PM, Richard Broadbent <
richard.broadben...@imperial.ac.uk> wrote:

> here is a simple example (for more complex ones see the existing
> residues in an aminoacids.rtp)
>
> assume molecule looks like
>
> A-B-C
>
> where the -'s are bonds
>
> with residues AAA, BBB, CCC containing the corresponding atoms,
> then the .rtp should contain something like:
>
> [ AAA ]
> [ atoms ]
>   A typeA  chargeA 1
> [ bonds ]
>   A +B
>
> [ BBB ]
> [ atoms ]
>   B typeB  chargeB 1
> [ bonds ]
>   B -A
>   B +C
>
> [ CCC ]
> [ atoms ]
>   C typeC  chargeC 1
> [ bonds ]
>   C -B
>
> the + and - define which direction the connection should go
>
> I hope that's helpful
>
> Richard
>
> On Fri, 2012-05-11 at 15:43 +0100, Steven Neumann wrote:
> > Dear Gromacs Users,
> >
> > I created my own residues in aminoacids.rtp which each is formed of
> > one atom. I would like to somehow create bonds between then using
> > standart harmonic potential. Could you please advise how to do this?
> >
> > Stevem
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

All right.
Thank you



 From: Anirban 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, May 11, 2012 8:11 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 9:10 PM, Anirban  wrote:


>
>
>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
>wrote:
>
>Dear gmx users,
>>
>>
>>I'm going to simulate the POPC in water.
>>I downloaded required files in Tielman site and made the .top file. Then 
>>included the CHARMM27.ff in the .top file.

Its better to use CHARMM36 FF. It is more accurate towards the lipids and 
available from the GROMACS user contribution section.
 
When I run the grompp I get the fatal error as below:
>>Atomtype CB not found
>>
>>
>>
>>I have done the same with gromos87.ff . But I didn't see any error.
>>What's the problem?
>>Anybody may suggest me how to solve this problem? Is this because of the 
>>forcefield? Or something in .top file goes wrong?
>>
>>
>
>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
>the Berger lipid parameters and have you included the POPC topology? You can 
>follow this tutorial to get an idea:
>
>https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
>-Anirban
> 
>Thanks,
>>Shima
>>
>>--
>>gmx-users mailing list    gmx-users@gromacs.org
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at 
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org.
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>-- 
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

Dear Anirban,
No, I have not done. Because I didn't know I need Berger lipids for this 
simulation. 

Thanks for you reply,
Cheers,
Shima




 From: Anirban 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Friday, May 11, 2012 8:10 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh  
wrote:

Dear gmx users,
>
>
>I'm going to simulate the POPC in water.
>I downloaded required files in Tielman site and made the .top file. Then 
>included the CHARMM27.ff in the .top file.
>When I run the grompp I get the fatal error as below:
>Atomtype CB not found
>
>
>
>I have done the same with gromos87.ff . But I didn't see any error.
>What's the problem?
>Anybody may suggest me how to solve this problem? Is this because of the 
>forcefield? Or something in .top file goes wrong?
>
>

Have properly edited the CHARMM27 bonded and nonbonded .itp files to include 
the Berger lipid parameters and have you included the POPC topology? You can 
follow this tutorial to get an idea:

https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial

-Anirban
 
Thanks,
>Shima
>
>--
>gmx-users mailing list    gmx-users@gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-requ...@gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Anirban]

On Fri, May 11, 2012 at 9:10 PM, Anirban wrote:

>
>
> On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
>> Dear gmx users,
>>
>> I'm going to simulate the POPC in water.
>> I downloaded required files in Tielman site and made the .top file. Then
>> included the CHARMM27.ff in the .top file.
>>
>
Its better to use CHARMM36 FF. It is more accurate towards the lipids and
available from the GROMACS user contribution section.


> When I run the grompp I get the fatal error as below:
>> Atomtype CB not found
>>
>> I have done the same with gromos87.ff . But I didn't see any error.
>> What's the problem?
>> Anybody may suggest me how to solve this problem? Is this because of the
>> forcefield? Or something in .top file goes wrong?
>>
>>
> Have properly edited the CHARMM27 bonded and nonbonded .itp files to
> include the Berger lipid parameters and have you included the POPC
> topology? You can follow this tutorial to get an idea:
>
> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
> -Anirban
>
>
>> Thanks,
>> Shima
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
-- 
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Re: [gmx-users] Create Bond between new residues

[Richard Broadbent]

here is a simple example (for more complex ones see the existing
residues in an aminoacids.rtp)

assume molecule looks like 

A-B-C

where the -'s are bonds

with residues AAA, BBB, CCC containing the corresponding atoms,
then the .rtp should contain something like:

[ AAA ]
[ atoms ]
   A typeA  chargeA 1
[ bonds ]
   A +B

[ BBB ]
[ atoms ]
   B typeB  chargeB 1
[ bonds ]
   B -A
   B +C

[ CCC ]
[ atoms ]
   C typeC  chargeC 1
[ bonds ]
   C -B

the + and - define which direction the connection should go

I hope that's helpful

Richard

On Fri, 2012-05-11 at 15:43 +0100, Steven Neumann wrote:
> Dear Gromacs Users,
> 
> I created my own residues in aminoacids.rtp which each is formed of
> one atom. I would like to somehow create bonds between then using
> standart harmonic potential. Could you please advise how to do this?
> 
> Stevem 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
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Re: [gmx-users] Simulation of POPC in water using CHARMM27

[Anirban]

On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh
wrote:

> Dear gmx users,
>
> I'm going to simulate the POPC in water.
> I downloaded required files in Tielman site and made the .top file. Then
> included the CHARMM27.ff in the .top file.
> When I run the grompp I get the fatal error as below:
> Atomtype CB not found
>
> I have done the same with gromos87.ff . But I didn't see any error.
> What's the problem?
> Anybody may suggest me how to solve this problem? Is this because of the
> forcefield? Or something in .top file goes wrong?
>
>
Have properly edited the CHARMM27 bonded and nonbonded .itp files to
include the Berger lipid parameters and have you included the POPC
topology? You can follow this tutorial to get an idea:

https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial

-Anirban


> Thanks,
> Shima
>
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[gmx-users] MPIRUN issue for CHARMM36 FF

[Anirban]

Hi ALL,

I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
mpirun and gives proper output. But whenever I try to submit it on more
than 5 nodes, the job gets killed with the following error:

-

starting mdrun 'Protein'
5000 steps, 10.0 ps.

NOTE: Turning on dynamic load balancing

Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error
Fatal error in MPI_Sendrecv: Other MPI error

=
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 256
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=
[proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed
[proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error
waiting for event
.
.
.
--

Why is this happening? Is it related to DD and PME? How to solve it? Any
suggestion is welcome.


Thanks and regards,

Anirban
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[gmx-users] Create Bond between new residues

[Steven Neumann]

Dear Gromacs Users,

I created my own residues in aminoacids.rtp which each is formed of one
atom. I would like to somehow create bonds between then using standart
harmonic potential. Could you please advise how to do this?

Stevem
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Re: [gmx-users] problem

[Richard Broadbent]

Dear Anik,

> Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
Is there a particular reason you are using such an old version of
gromacs? 

If not then switch to the latest version as there have been many
improvements

> 
>   I was trying to run the dynamics for some inorganic metal
> halides solvation in water. A fatal error is comingthat:
>   * Atomtype "CH2r" not found. 
This is not enough information to let us help you please include the
command you ran. e.g. "$ grompp -f mdout.mdp -c conf.gro -p topol.top"
and all the relevant lines of the output.

> But in my system I have no such atoms. Only water molecules with tip4p
> model and the inorganic metal halides. So please can anyone state
> whats the problem. 
Assuming this error is occuring from grompp it suggests that there is
such an atom in your system check the [ atoms ] section in your .top
file and also the atom names in your .gro file.

Regards,

Richard

> 
> Thanking in advance
> Anik Sen
> 
> 
> Anik Sen
> Student
> CSIR-Central Salt & Marine Chemicals Research Institute,
> Gijubhai Badheka Marg.
> Bhavnagar, Gujarat 364002
> www.csmcri.org
> 
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[gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

Dear gmx users,

I'm going to simulate the POPC in water.
I downloaded required files in Tielman site and made the .top file. Then 
included the CHARMM27.ff in the .top file.
When I run the grompp I get the fatal error as below:
Atomtype CB not found


I have done the same with gromos87.ff . But I didn't see any error.
What's the problem?
Anybody may suggest me how to solve this problem? Is this because of the 
forcefield? Or something in .top file goes wrong?

Thanks,
Shima
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Re: [gmx-users] problem

[Terry]

You should paste your topology for you metal halides so that others can
help.



On Fri, May 11, 2012 at 9:48 PM, Anik Sen  wrote:

>  Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
>
>   I was trying to run the dynamics for some inorganic metal
> halides solvation in water. A fatal error is comingthat:
>
>- Atomtype "CH2r" not found.
>
> But in my system I have no such atoms. Only water molecules with tip4p
> model and the inorganic metal halides. So please can anyone state whats the
> problem.
>
> Thanking in advance
> Anik Sen
>  
> Anik Sen
> Student
> CSIR-Central Salt & Marine Chemicals Research Institute,
> Gijubhai Badheka Marg.
> Bhavnagar, Gujarat 364002
> [image: www.csmcri.org]
> 
>
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[gmx-users] problem

[Anik Sen]

Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.

  I was trying to run the dynamics for some inorganic metal halides 
solvation in water. A fatal error is comingthat:

  *   Atomtype "CH2r" not found.

But in my system I have no such atoms. Only water molecules with tip4p model 
and the inorganic metal halides. So please can anyone state whats the problem.

Thanking in advance
Anik Sen
[X][X]

Anik Sen
Student
CSIR-Central Salt & Marine Chemicals Research Institute,
Gijubhai Badheka Marg.
Bhavnagar, Gujarat 364002
[www.csmcri.org]

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Re: [gmx-users] movement in 2 directions - remove one degree of freedom

[Erik Marklund]

11 maj 2012 kl. 14.38 skrev Steven Neumann:

> Dear Gromacs Users,
> 
> Is there any way in Gromacs which will allow me to contraint some of the 
> atoms in the system to move only in the coordinate X and Z? I do not want 
> some of my atoms to move in Y direction. Do you know how to do this?
> 

Hi,

Not exactly. But you can apply position restraints with zero force constants  
in X and Z directions. This will allow some movement in the Y direction, but 
the extent depends on your force constant in the Y direction.

Erik

> Steven
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] movement in 2 directions - remove one degree of freedom

[Steven Neumann]

Dear Gromacs Users,

Is there any way in Gromacs which will allow me to contraint some of the
atoms in the system to move only in the coordinate X and Z? I do not want
some of my atoms to move in Y direction. Do you know how to do this?

Steven
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[gmx-users] solvent group size (12548) is not a multiple of 3

[Sangita Kachhap]

protein
>> cat KALP_newbox.gro popc128a_whole.gro > system.gro
>> Remove unnecessary lines (the box vectors from the KALP structure, the
>> header
>> information from the DPPC structure) and update the second line of the
>> coordinate file (total number of atoms) accordingly.
>>
>>
>> 9) Modify topol.top to add positional restrain on protein
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Strong position restraints for InflateGRO
>> #ifdef STRONG_POSRES
>> #include "strong_posre.itp"
>> #endif
>>
>> ; Include DPPC chain topology
>> #include "dppc.itp"
>>
>> ; Include water topology
>> #include "gromos53a6_lipid.ff/spc.itp"
>>
>> &
>>
>> Genrate new positional restraint
>> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10
>> (at prompt select 2)
>>
>> Add a line "define = -DSTRONG_POSRES" to .mdp file
>>
>>
>>
>>
>> 10) Scale down lipid
>> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5
>> area_shrink1.dat
>> system_shrink1.gro
>>
>>
>> 11) addion POPC 128 to topol.top
>>
>>
>> 12) Solvate with water
>> Copy vdwradii.dat from Gromacs top to working directory and change the
>> value of
>> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>>
>> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
>> topol.top
>>
>>
>> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr
>>
>> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
>> CL -nn 4
>> (at command prompt select 0)
>>
>
> Is group 0 your solvent? You should chose a group corresponding to the
> solvent of your system.


Thans for reply. I got it its 15 not 0, now its working fine.





>
>
>
>>
>>
>>
>> So can anyone please help me correct this error.
>>
>>
>>
>> With regards
>> Sangita Kachhap
>> SRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> __
>> ??�??? ???�
>> ? (??? 
>>  ???)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> ?? 39 ???, ??�? / Sector 39-A, Chandigarh
>> ? ?/PIN CODE :160036
>> ??/EPABX :0172 6665 201-202
>> --
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>
> End of gmx-users Digest, Vol 97, Issue 71
> *
>


Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH

__
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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[gmx-users] Martini mapping for fluorinated alkane

[maria goranovic]

I have a fully fluorinated alkane, and am wondering how to choose the right
atom-to-bead mapping. 4 CH2 groups form a C1 bead in Martini. Will CF2-CF2
(6 heavy atoms), also map to a C1 bead type? How does one go about making
the right choice?

Any suggestions will be so welcome

-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] rvdw and DispCorr

[Dommert Florian]

On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote: 
> Dear gromacs users
> 
> In a recent paper I found the following protocol of a gromacs simulation:
> 
> "All simulations were performed with the GROMACS 4.0 [12] compiled in 
> single-precision mode at a constant temperature of 277 K in a periodic box 
> with an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 
> forcefield [22]. The simulation systems each contained approximately 16,500 
> Simple Point Charge (SPC) water molecules [23]. Short-range interactions were 
> evaluated using a neighbor list of 1.0 nm updated at every 10 steps. Van der 
> Waals interactions used a cutoff with a smoothing 
> function such that the interactions slowly decayed to zero between 0.75 nm 
> and 0.90 nm. A long-range analytical dispersion correction was applied to the 
> energy and pressure to account for the truncation of the Lennard-Jones 
> interactions [24]. Electrostatic interactions were evaluated using the 
> particle mesh Ewald (PME) [25] with a real space cutoff of 1.0 nm, a spline 
> order of 6, a Fourier spacing of 0.1 m, and relative tolerance between long 
> and short range energies of . All bonds to hydrogen 
> were constrained with LINCS [26] with an order of 12, and a time step of 2 fs 
> was used for dynamics."
> 
> In the gromacs manual 4.5.4, page 104 it says: "The GROMOS-96 force field was 
> parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a 
> Lennard-Jones cut-off (rvdw) of at least 1.4".
> 
> Is it a good idea to set "DispCorr" to "EnerPres" and reduce the rvdw so 
> dramatically (almost the half value)?
> 

This depends on the sensitivity of force field to these settings. I
would try different cut-offs and compare some properties like the mass
density. In my studies I often realized that already a small change in
the cutoff ~0.1nm may give really different results, though a dispersion
correction is applied. This is a results from the procedure, the force
field is constructed. Usually all force field parameters are highly
correlated.  

> And a second question: Is there a study on the percentage of information 
> getting lost when reducing the rvdw with and without dispcorr (e.g. to 1.2, 
> 1.0, etc) if the forcefield was parameterized with 1.4?
> 

So I would expect, that if the system is already homogeneous at rc=0.9
and dispersion correction is applied, a further increase rc should give
the same results. However, if the system is not homogeneous at rc, an
increase in rc provides more information about the systems.


Actually, if there is no very good reason, to chose another cut-off for
LJ, as suggested by the force field authors, I would not change it.
However, if the homogeneity requirement is met, an small decrease of the
cut-off should not introduce too large artefacts. Always keep in mind,
that all force field parameters are highly correlated, which includes
also the cut-offs, switching or shifting methods, combination
rules, ... . The only parameters, where you often have some freedom
regard to electrostatics, in case no reaction field method is applied,
because then similar considerations as for the LJ cut-off apply. However
if an explicit calculation over all charges is used, like in Ewald-based
methods, you only have to assure that your settings conform to a certain
accuracy, given during the force field parametrization.

Cheers,
Flo





> best,
> Bernhard
> 
> 
> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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[gmx-users] line longer than 4095 - a bug?

[Marzinek, Jan]

Dear Gmx Users,

Many of you probably faced an error:

"An input file contains a line longer than 4095 characters, while the buffer 
passed to fgets2 has size 4095. The line starts with: '20s' "

As I noted this error comes from the changes in the topology. Gromacs somehow 
add " _ " and thus this problem occurs. For instance:


[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
1 3 1
1 4 1
4 5 1
4 6 1 _
424 1
6 7 1

I could not see " _ " using vi in my topology. However, when I copied all 
topology to another text editor I could. Then removing it solves the problem. 
Is that a bug?
This is just to inform people for the future as I have spent many hours to find 
out what is wrong.

Best,

Jan

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Re: [gmx-users] solvent group size (12548) is not a multiple of 3

[Terry]

On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap wrote:

>
> Hello all
> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
> I am geeting error during addiotion of ions
> Fatal error:
> Your solvent group size (12548) is not a multiple of 3
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> I have done following:
>
> GROMACS COMMAND
>
> 1) Generate topol.top using GROMOS96 53A6 parameter set
> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
>
> ay prompt select 13, 2, 2
>
> 2) Download:
>* dppc128.pdb - the structure of a 128-lipid DPPC bilayer
>* dppc.itp - the moleculetype definition for DPPC
>* lipid.itp - Berger lipid parameters
>
> from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> 3) Modify topol.top with:
> #include "gromos53a6.ff/forcefield.itp"
>
> to:
>
> #include "gromos53a6_lipid.ff/forcefield.itp"
>
>
>&
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
>
>
> 4) cp files
> aminoacids.rtp
> aminoacids.hdb
> aminoacids.c.tdb
> aminoacids.n.tdb
> aminoacids.r2b
> aminoacids.vsd
> ff_dum.itp
> ffnonbonded.itp
> ffbonded.itp
> forcefield.itp
> ions.itp
> spc.itp
> watermodels.dat
>
> from gromacs top to directory named gromos53a6_lipid.ff in working
> directory.
> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
> lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc
> file
> that contains a description of the force field parameters contain
> "GROMOS96 53A6
> force field, extended to include Berger lipid parameters".
> Delete line ";; parameters for lipid-GROMOS interactions." and its
> subsequent
> line, change HW as H of [ nonbond_params ]
>
>
> 5) Generate .tpr for POPC
> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)
>
>
> 6) Remove periodicity
> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur
> compact
> (at command prompt select 0)
>
>
> 7) Oriant the KALP peptide within the same coordinate as written in end of
> popc128a_whole.gro
> editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.23910
> 6.17970
> 6.91950
>
>
> 8) Pack lipid around protein
> cat KALP_newbox.gro popc128a_whole.gro > system.gro
> Remove unnecessary lines (the box vectors from the KALP structure, the
> header
> information from the DPPC structure) and update the second line of the
> coordinate file (total number of atoms) accordingly.
>
>
> 9) Modify topol.top to add positional restrain on protein
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
> ; Include water topology
> #include "gromos53a6_lipid.ff/spc.itp"
>
> &
>
> Genrate new positional restraint
> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10
> (at prompt select 2)
>
> Add a line "define = -DSTRONG_POSRES" to .mdp file
>
>
>
>
> 10) Scale down lipid
> perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5
> area_shrink1.dat
> system_shrink1.gro
>
>
> 11) addion POPC 128 to topol.top
>
>
> 12) Solvate with water
> Copy vdwradii.dat from Gromacs top to working directory and change the
> value of
> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)
>
> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p
> topol.top
>
>
> grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr
>
> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
> CL -nn 4
> (at command prompt select 0)
>

Is group 0 your solvent? You should chose a group corresponding to the
solvent of your system.



>
>
>
> So can anyone please help me correct this error.
>
>
>
> With regards
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> __
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
> --
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[gmx-users] rvdw and DispCorr

[Bernhard Knapp]

Dear gromacs users

In a recent paper I found the following protocol of a gromacs simulation:

"All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 forcefield [22]. The simulation systems each contained approximately 16,500 Simple Point Charge (SPC) water molecules [23]. Short-range interactions were evaluated using a neighbor list of 1.0 nm updated at every 10 steps. Van der Waals interactions used a cutoff with a smoothing 
function such that the interactions slowly decayed to zero between 0.75 nm and 0.90 nm. A long-range analytical dispersion correction was applied to the energy and pressure to account for the truncation of the Lennard-Jones interactions [24]. Electrostatic interactions were evaluated using the particle mesh Ewald (PME) [25] with a real space cutoff of 1.0 nm, a spline order of 6, a Fourier spacing of 0.1 m, and relative tolerance between long and short range energies of . All bonds to hydrogen 
were constrained with LINCS [26] with an order of 12, and a time step of 2 fs was used for dynamics."


In the gromacs manual 4.5.4, page 104 it says: "The GROMOS-96 force field was 
parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a Lennard-Jones 
cut-off (rvdw) of at least 1.4".

Is it a good idea to set "DispCorr" to "EnerPres" and reduce the rvdw so 
dramatically (almost the half value)?

And a second question: Is there a study on the percentage of information 
getting lost when reducing the rvdw with and without dispcorr (e.g. to 1.2, 
1.0, etc) if the forcefield was parameterized with 1.4?

best,
Bernhard



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