Re: [gmx-users] QMMM number of thread

[Javier Cerezo]

1.- You can only run the MD part in 1 thread, but you can perform the QM 
step with more procs. Note that, except for MOPAC, for which the library 
libmopac (see instructions in the website for how to get this) is 
directly used by the GROMACS code, the QM part consists in a external 
call to the QM package. In this call, you can use as many procs as you 
would use in any other call to the QM program.


2.- As said avobe, yes, the QM program manages its threads and memory 
independently, as it is a external call (except for MOPAC).


3.- Needs third party software (Gaussian, ORCA...) or the libmopac 
library provided at compilaton time.


Javier


El 19/07/13 08:49, SEMRAN İPEK escribió:

Dear Users;


I would like to use Gromacs for QM/MM calculations. Up to now md
calculations have been proceed without failure. Could you please shed on
light on these issues related to the number of threads while using QM/MM
interface with any kind of Quantum Chemistry software?
1-How many thread could be used during QM/MM calculation in Gromacs?
2-Does number of threads that are available for calculations depend on the
software used for QM?
3-Can GROMACS handle QM/MM calculations by its own or need other simulation
package (such as Gaussian, MOPAC, GAMESS) for QM/MM part?

I am looking forward your kindly advices.


regards,

semran ipek küskü
Istanbul Medeniyet University
Engineering Physics Dept.
ISTANBUL-TURKEI


--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] QMMM number of thread

[SEMRAN İPEK]

Dear Javier;


Thanks for comprehensive explanations for elusive part of QM/MM
calculations.

Best Regards,

semran


2013/7/19 Javier Cerezo 

>
> 1.- You can only run the MD part in 1 thread, but you can perform the QM
> step with more procs. Note that, except for MOPAC, for which the library
> libmopac (see instructions in the website for how to get this) is directly
> used by the GROMACS code, the QM part consists in a external call to the QM
> package. In this call, you can use as many procs as you would use in any
> other call to the QM program.
>
> 2.- As said avobe, yes, the QM program manages its threads and memory
> independently, as it is a external call (except for MOPAC).
>
> 3.- Needs third party software (Gaussian, ORCA...) or the libmopac library
> provided at compilaton time.
>
> Javier
>
>
> El 19/07/13 08:49, SEMRAN İPEK escribió:
>
>  Dear Users;
>>
>>
>> I would like to use Gromacs for QM/MM calculations. Up to now md
>> calculations have been proceed without failure. Could you please shed on
>> light on these issues related to the number of threads while using QM/MM
>> interface with any kind of Quantum Chemistry software?
>> 1-How many thread could be used during QM/MM calculation in Gromacs?
>> 2-Does number of threads that are available for calculations depend on the
>> software used for QM?
>> 3-Can GROMACS handle QM/MM calculations by its own or need other
>> simulation
>> package (such as Gaussian, MOPAC, GAMESS) for QM/MM part?
>>
>> I am looking forward your kindly advices.
>>
>>
>> regards,
>>
>> semran ipek küskü
>> Istanbul Medeniyet University
>> Engineering Physics Dept.
>> ISTANBUL-TURKEI
>>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
> --
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Re: [gmx-users] g_hbond for trajectory without having box information

[bipin singh]

According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:

trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc

then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-bonds between the proteins
atoms.

I have also tried to process the output trajectory (traj_box.xtc) with
trjconv using -pbc mol -ur compact options before using g_hbond, but again
I have got wrong number of H-bonds.

Please help me to rectify the error.


On Fri, Jul 19, 2013 at 11:19 AM, bipin singh  wrote:

> Thanks a lot Prof. David. I will try this.
>
>
> On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
> sp...@xray.bmc.uu.se> wrote:
>
>> On 2013-07-19 06:26, bipin singh wrote:
>>
>>> Hello all,
>>>
>>> I was using g_hbond to calculate H-bonds for a trajectory made from
>>> several
>>> individual snapshots from MD simulation, but because this trajectory does
>>> not have the coordinates/information for simulation box, g_hbond is
>>> giving
>>> the following error:
>>>
>>> Fatal error:
>>> Your computational box has shrunk too much.
>>> g_hbond_mpi can not handle this situation, sorry.
>>>
>>>
>>> Please let me know, if there is any way to rectify this error.
>>>
>>>
>>>  you can add a box to your trajectory using trjconv.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
>
> --
> *---
> Thanks and Regards,
> Bipin Singh*
>



-- 
*---
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Bipin Singh*
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Re: [gmx-users] g_hbond for trajectory without having box information

[Justin Lemkul]

On 7/19/13 4:17 AM, bipin singh wrote:

According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:

trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc

then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-bonds between the proteins
atoms.

I have also tried to process the output trajectory (traj_box.xtc) with
trjconv using -pbc mol -ur compact options before using g_hbond, but again
I have got wrong number of H-bonds.

Please help me to rectify the error.



A 0.9-nm cubic box is likely too small to correctly accommodate even an amino 
acid, let alone an entire protein.


-Justin



On Fri, Jul 19, 2013 at 11:19 AM, bipin singh  wrote:


Thanks a lot Prof. David. I will try this.


On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
sp...@xray.bmc.uu.se> wrote:


On 2013-07-19 06:26, bipin singh wrote:


Hello all,

I was using g_hbond to calculate H-bonds for a trajectory made from
several
individual snapshots from MD simulation, but because this trajectory does
not have the coordinates/information for simulation box, g_hbond is
giving
the following error:

Fatal error:
Your computational box has shrunk too much.
g_hbond_mpi can not handle this situation, sorry.


Please let me know, if there is any way to rectify this error.


  you can add a box to your trajectory using trjconv.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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--
*---
Thanks and Regards,
Bipin Singh*







--
==

Justin A. Lemkul, Ph.D.
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

==
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Aw: Re: [gmx-users] How to calculate enthalpy

[lloyd riggs]

 

I thought about this reguaring solvation energy.  If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2.  I assume you could do some extreemly accurate solvation energy calculations this way, but the guassians for say 10-20 parallel runs of the same system would be much greater than say a protein-protein interaction.  I am sure solvent models would have to be good as well, but may allow you to do what you wished, however I would make sure through others first, and I do not know what you wished to do completly.

 

Stephan Watkins


Gesendet: Montag, 15. Juli 2013 um 19:25 Uhr
Von: "lloyd riggs" 
An: "Discussion list for GROMACS users" 
Betreff: Aw: Re: [gmx-users] How to calculate enthalpy



Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)?  And the energy of the internal structural hydrogen bonds that were disrupted?  Assuming no acidic enviornment where electrons are involved...means of coarse...
 

Gesendet: Montag, 15. Juli 2013 um 10:34 Uhr
Von: pooja_gu...@nccs.res.in
An: vvcha...@gmail.com, "Discussion list for GROMACS users" 
Betreff: Re: [gmx-users] How to calculate enthalpy

Thanks Vitaly

but how??

let's say the difference between unfolded to folded protein is 100 water
molecules. What is the correct procedure to calculate (theoretically) the
entrapy correspond to single water molecule for stabilizing/destabilizing
the protein.

help me

> Sure, you can.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jul 15, 2013 at 8:38 AM,  wrote:
>
>> Hi
>>
>> I want calculate the enthalpy of water molecule corresponding to protein
>> folded and unfolded state.
>> How much a single water molecule (enthalpy and free energy) contribute
>> in
>> folding ?
>> Can we calculate enthapy from g_energy?
>>
>>
>>
>> --
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Re: [gmx-users] g_hbond for trajectory without having box information

[bipin singh]

Sorry for my silly mistake.

I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.

 I mean, will the number of H-bonds present at a particular time in a MD
trajectory (protein+solvent), should be exactly same as number of H-bonds
calculated using trajectory made of concatenated frames (only protein) from
(if we look at number of H-bonds present at same point of time in both).

Because I am not getting the exact match between the two, there is random
difference of 1-3 H-bonds at some point of time.


On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul  wrote:

>
>
> On 7/19/13 4:17 AM, bipin singh wrote:
>
>> According to the suggestion I added the box to the trajectory using -box
>> option of trjconv, using the following commands:
>>
>> trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc
>>
>> then using the g_hbond on the output trjectory (traj_box.xtc) run
>> successfully but gives the wrong number of H-bonds between the proteins
>> atoms.
>>
>> I have also tried to process the output trajectory (traj_box.xtc) with
>> trjconv using -pbc mol -ur compact options before using g_hbond, but again
>> I have got wrong number of H-bonds.
>>
>> Please help me to rectify the error.
>>
>>
> A 0.9-nm cubic box is likely too small to correctly accommodate even an
> amino acid, let alone an entire protein.
>
> -Justin
>
>
>> On Fri, Jul 19, 2013 at 11:19 AM, bipin singh 
>> wrote:
>>
>>  Thanks a lot Prof. David. I will try this.
>>>
>>>
>>> On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
>>> sp...@xray.bmc.uu.se> wrote:
>>>
>>>  On 2013-07-19 06:26, bipin singh wrote:

  Hello all,
>
> I was using g_hbond to calculate H-bonds for a trajectory made from
> several
> individual snapshots from MD simulation, but because this trajectory
> does
> not have the coordinates/information for simulation box, g_hbond is
> giving
> the following error:
>
> Fatal error:
> Your computational box has shrunk too much.
> g_hbond_mpi can not handle this situation, sorry.
>
>
> Please let me know, if there is any way to rectify this error.
>
>
>   you can add a box to your trajectory using trjconv.
>

 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell & Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
 sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users>
 >
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Search>>> Mailing_Lists/Search>before
 posting!

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 interface or send it to gmx-users-requ...@gromacs.org.
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 http://www.gromacs.org/Support/Mailing_Lists
 
 >


>>>
>>>
>>> --
>>> *---
>>> Thanks and Regards,
>>> Bipin Singh*
>>>
>>>
>>
>>
>>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> 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
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
*---
Thanks and Regards,
Bipin Singh*
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[gmx-users] GROMACS 4.6.3 Static Linking

[Andrew R Turner]

Hi

I am having problems creating static versions of the GROMACS binaries  
for a Cray XE6 (www.hector.ac.uk). The build process I am using is  
documented at:


http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php

and successfully produced static binaries for 4.6.1. Has something  
changed in the new version?


In particular, I am setting:

-DCMAKE_SKIP_RPATH=YES
-DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DCMAKE_C_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
-DCMAKE_CXX_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"

but still get dynamic executables:

gmx@hector-xe6-5:~/4.6.3-phase3/bin> ldd grompp
linux-vdso.so.1 =>  (0x7fff00da2000)
libm.so.6 => /lib64/libm.so.6 (0x7f50dc58f000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x7f50dc371000)
	libAtpSigHandler.so.0 => /opt/cray/lib64/libAtpSigHandler.so.0  
(0x7f50dc16b000)
	libgfortran.so.3 => /opt/gcc/4.7.2/snos/lib64/libgfortran.so.3  
(0x7f50dbe54000)

libscicpp_gnu.so.2 => /opt/cray/lib64/libscicpp_gnu.so.2 
(0x7f50dbc4a000)
libsci_gnu_mp.so.2 => /opt/cray/lib64/libsci_gnu_mp.so.2 
(0x7f50d72ec000)
	libstdc++.so.6 => /opt/gcc/4.7.2/snos/lib64/libstdc++.so.6  
(0x7f50d6fdf000)

libfftw3_mpi.so.3 => /opt/cray/lib64/libfftw3_mpi.so.3 
(0x7f50d6dc6000)
libfftw3f_mpi.so.3 => /opt/cray/lib64/libfftw3f_mpi.so.3 
(0x7f50d6bae000)
	libfftw3_threads.so.3 => /opt/cray/lib64/libfftw3_threads.so.3  
(0x7f50d69a6000)
	libfftw3f_threads.so.3 => /opt/cray/lib64/libfftw3f_threads.so.3  
(0x7f50d679d000)

libfftw3.so.3 => /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000)
libfftw3f.so.3 => /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000)
	libmpich_gnu_47.so.1 => /opt/cray/lib64/libmpich_gnu_47.so.1  
(0x7f50d5add000)
	libmpichf90_gnu_47.so.1 => /opt/cray/lib64/libmpichf90_gnu_47.so.1  
(0x7f50d58da000)

libmpl.so.0 => /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000)
librt.so.1 => /lib64/librt.so.1 (0x7f50d54cb000)
	libxpmem.so.0 => /opt/cray/xpmem/default/lib64/libxpmem.so.0  
(0x7f50d52c9000)
	libdmapp.so.1 => /opt/cray/dmapp/default/lib64/libdmapp.so.1  
(0x7f50d5092000)
	libugni.so.0 => /opt/cray/ugni/default/lib64/libugni.so.0  
(0x7f50d4e72000)

libpmi.so.0 => /opt/cray/pmi/default/lib64/libpmi.so.0 
(0x7f50d4c51000)
libalpslli.so.0 => /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000)
libalpsutil.so.0 => /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000)
	libudreg.so.0 => /opt/cray/udreg/default/lib64/libudreg.so.0  
(0x7f50d4641000)

libgomp.so.1 => /opt/gcc/4.7.2/snos/lib64/libgomp.so.1 
(0x7f50d4432000)
libc.so.6 => /lib64/libc.so.6 (0x7f50d40d3000)
libgcc_s.so.1 => /opt/gcc/4.7.2/snos/lib64/libgcc_s.so.1 
(0x7f50d3ebd000)
/lib/ld64.so.1 => /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000)
	libquadmath.so.0 => /opt/gcc/4.7.2/snos/lib64/libquadmath.so.0  
(0x7f50d3c87000)
	libcray_memcpy.so.0 => /opt/cray/lib64/libcray_memcpy.so.0  
(0x7f50d3a84000)

libopa.so.1 => /opt/cray/lib64/libopa.so.1 (0x7f50d3882000)
librca.so.0 => /opt/cray/rca/default/lib64/librca.so.0 
(0x7f50d367d000)
libdl.so.2 => /lib64/libdl.so.2 (0x7f50d3479000)

Any ideas?
Andy


=
Dr Andrew R. Turner
 e: a.tur...@epcc.ed.ac.uk
 skype: aturner-epcc
 t: +44 (0)131 651 3578
 p: EPCC, University of Edinburgh EH9 3JZ
=

--
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Scotland, with registration number SC005336.


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Re: [gmx-users] GROMACS 4.6.3 Static Linking

[Mark Abraham]

What does build_*/src/buildinfo.h have to say about the compiler flags
that are getting used?

Mark

On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner
 wrote:
> Hi
>
> I am having problems creating static versions of the GROMACS binaries for a
> Cray XE6 (www.hector.ac.uk). The build process I am using is documented at:
>
> http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php
>
> and successfully produced static binaries for 4.6.1. Has something changed
> in the new version?
>
> In particular, I am setting:
>
> -DCMAKE_SKIP_RPATH=YES
> -DBUILD_SHARED_LIBS=OFF
> -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
> -DCMAKE_CXX_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
>
> but still get dynamic executables:
>
> gmx@hector-xe6-5:~/4.6.3-phase3/bin> ldd grompp
> linux-vdso.so.1 =>  (0x7fff00da2000)
> libm.so.6 => /lib64/libm.so.6 (0x7f50dc58f000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x7f50dc371000)
> libAtpSigHandler.so.0 => /opt/cray/lib64/libAtpSigHandler.so.0
> (0x7f50dc16b000)
> libgfortran.so.3 => /opt/gcc/4.7.2/snos/lib64/libgfortran.so.3
> (0x7f50dbe54000)
> libscicpp_gnu.so.2 => /opt/cray/lib64/libscicpp_gnu.so.2
> (0x7f50dbc4a000)
> libsci_gnu_mp.so.2 => /opt/cray/lib64/libsci_gnu_mp.so.2
> (0x7f50d72ec000)
> libstdc++.so.6 => /opt/gcc/4.7.2/snos/lib64/libstdc++.so.6
> (0x7f50d6fdf000)
> libfftw3_mpi.so.3 => /opt/cray/lib64/libfftw3_mpi.so.3
> (0x7f50d6dc6000)
> libfftw3f_mpi.so.3 => /opt/cray/lib64/libfftw3f_mpi.so.3
> (0x7f50d6bae000)
> libfftw3_threads.so.3 => /opt/cray/lib64/libfftw3_threads.so.3
> (0x7f50d69a6000)
> libfftw3f_threads.so.3 => /opt/cray/lib64/libfftw3f_threads.so.3
> (0x7f50d679d000)
> libfftw3.so.3 => /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000)
> libfftw3f.so.3 => /opt/cray/lib64/libfftw3f.so.3
> (0x7f50d5f7c000)
> libmpich_gnu_47.so.1 => /opt/cray/lib64/libmpich_gnu_47.so.1
> (0x7f50d5add000)
> libmpichf90_gnu_47.so.1 => /opt/cray/lib64/libmpichf90_gnu_47.so.1
> (0x7f50d58da000)
> libmpl.so.0 => /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000)
> librt.so.1 => /lib64/librt.so.1 (0x7f50d54cb000)
> libxpmem.so.0 => /opt/cray/xpmem/default/lib64/libxpmem.so.0
> (0x7f50d52c9000)
> libdmapp.so.1 => /opt/cray/dmapp/default/lib64/libdmapp.so.1
> (0x7f50d5092000)
> libugni.so.0 => /opt/cray/ugni/default/lib64/libugni.so.0
> (0x7f50d4e72000)
> libpmi.so.0 => /opt/cray/pmi/default/lib64/libpmi.so.0
> (0x7f50d4c51000)
> libalpslli.so.0 => /usr/lib/alps/libalpslli.so.0
> (0x7f50d4a4e000)
> libalpsutil.so.0 => /usr/lib/alps/libalpsutil.so.0
> (0x7f50d4849000)
> libudreg.so.0 => /opt/cray/udreg/default/lib64/libudreg.so.0
> (0x7f50d4641000)
> libgomp.so.1 => /opt/gcc/4.7.2/snos/lib64/libgomp.so.1
> (0x7f50d4432000)
> libc.so.6 => /lib64/libc.so.6 (0x7f50d40d3000)
> libgcc_s.so.1 => /opt/gcc/4.7.2/snos/lib64/libgcc_s.so.1
> (0x7f50d3ebd000)
> /lib/ld64.so.1 => /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000)
> libquadmath.so.0 => /opt/gcc/4.7.2/snos/lib64/libquadmath.so.0
> (0x7f50d3c87000)
> libcray_memcpy.so.0 => /opt/cray/lib64/libcray_memcpy.so.0
> (0x7f50d3a84000)
> libopa.so.1 => /opt/cray/lib64/libopa.so.1 (0x7f50d3882000)
> librca.so.0 => /opt/cray/rca/default/lib64/librca.so.0
> (0x7f50d367d000)
> libdl.so.2 => /lib64/libdl.so.2 (0x7f50d3479000)
>
> Any ideas?
> Andy
>
>
> =
> Dr Andrew R. Turner
>  e: a.tur...@epcc.ed.ac.uk
>  skype: aturner-epcc
>  t: +44 (0)131 651 3578
>  p: EPCC, University of Edinburgh EH9 3JZ
> =
>
> --
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> Scotland, with registration number SC005336.
>
>
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Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

[Mark Abraham]

What's the simplest case you can make work?

Mark

On Fri, Jul 19, 2013 at 8:38 AM, Éric Germaneau  wrote:
> I actually submitted  using two MPI process per node but log files do not
> get updated, it's like the calculation gets stuck.
>
> Here is how I proceed:
>
>mpirun -np $NM -machinefile nodegpu mdrun_mpi  -nb gpu -v -deffnm
>test184000atoms_verlet.tpr >& mdrun_mpi.log
>
> with the content of /nodegpu/:
>
>gpu04
>gpu04
>gpu11
>gpu11
>
> and with
>
>NM=`cat nodegpu | wc -l`
>
> /bjobs/ gives
>
>3983hpceric RUN   gpu mu0516*gpu11gromacsJul 19
>12:12
>16*gpu04
>
> /mdrun_mpi.log/ contains the description of the options and
> /test184000atoms_verlet.tpr.log/ stops after "PLEASE READ AND CITE THE
> FOLLOWING REFERENCE".
>
> The top of /test184000atoms_verlet.tpr.log/ is:
>
>Log file opened on Fri Jul 19 13:47:36 2013
>Host: gpu11  pid: 124677  nodeid: 0  nnodes:  4
>Gromacs version:VERSION 4.6.3
>Precision:  single
>Memory model:   64 bit
>MPI library:MPI
>OpenMP support: enabled
>GPU support:enabled
>invsqrt routine:gmx_software_invsqrt(x)
>CPU acceleration:   AVX_256
>FFT library:fftw-3.3.3-sse2-avx
>Large file support: enabled
>RDTSCP usage:   enabled
>Built on:   Mon Jul 15 13:44:42 CST 2013
>Built by:   name@node [CMAKE]
>Build OS/arch:  Linux 2.6.32-279.el6.x86_64 x86_64
>Build CPU vendor:   GenuineIntel
>Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
>Build CPU family:   6   Model: 45   Stepping: 7
>Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx
>msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2
>sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>C compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicc
>GNU gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
>C compiler flags:   -mavx-Wextra -Wno-missing-field-initializers
>-Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops  -O3 -DNDEBUG
>C++ compiler:
>/lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicxx GNU g++
>(GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
>C++ compiler flags: -mavx   -Wextra -Wno-missing-field-initializers
>-Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops  -O3 -DNDEBUG
>CUDA compiler:  /lustre/utility/cuda-5.0/bin/nvcc nvcc: NVIDIA
>(R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA
>Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation
>tools, release 5.0, V0.2.1221
>CUDA compiler
>
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-Xcompiler;-fPIC
>;
>
> -mavx;-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-fomit-frame-pointer;-funroll-all-loops;-O3;-DNDEBUG
>CUDA driver:5.0
>CUDA runtime:   5.0
>
> Does any have any idea about what's going wrong here?
> Thanks,
>
>  Éric.
>
>
> On 07/19/2013 09:35 AM, Éric Germaneau wrote:
>>
>> Dear all,
>>
>> I'm note a gromacs user,  I've installed gromacs 4.6.3 on our cluster and
>> making some test.
>> Each node of our machine has 16 cores and 2 GPU.
>> I'm trying to figure how to submit efficient multiple nodes LSF jobs using
>> the maximum of resources.
>> After reading the documentation
>> 
>> on "Acceleration and parallelization" I got confused and inquire some help.
>> I'm just wondering whether someone with some experiences on this matter.
>> I thank you in advance,
>>
>> Éric.
>>
>
> --
> /Be the change you wish to see in the world
> / --- Mahatma Gandhi ---
>
> Éric Germaneau 
>
> Shanghai Jiao Tong University
> Network & Information Center
> room 205
> Minhang Campus
> 800 Dongchuan Road
> Shanghai 200240
> China
>
> View Éric Germaneau's profile on LinkedIn
> 
>
> /Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>
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Re: [gmx-users] GROMACS 4.6.3 Static Linking

[Andrew R Turner]

Hi Mark,



What does build_*/src/buildinfo.h have to say about the compiler flags
that are getting used?


/** C compiler flags used to build */
#define BUILD_CFLAGS"-msse2-Wextra  
-Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused  
-Wunused-value  -static -O3 -ftree-ve
ctorize -ffast-math -funroll-loops -fomit-frame-pointer  
-funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG"



Cheers
Andy

=
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 e: a.tur...@epcc.ed.ac.uk
 skype: aturner-epcc
 t: +44 (0)131 651 3578
 p: EPCC, University of Edinburgh EH9 3JZ
=

--
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Re: [gmx-users] g_hbond for trajectory without having box information

[Justin Lemkul]

On 7/19/13 6:55 AM, bipin singh wrote:

Sorry for my silly mistake.

I have a doubt regarding the expected difference in total No. of H-bonds
calculated with whole a MD trajectory (protein+solvent box) and H-bonds
calculated with concatenated frames (only protein) from a MD trajectory.

  I mean, will the number of H-bonds present at a particular time in a MD
trajectory (protein+solvent), should be exactly same as number of H-bonds
calculated using trajectory made of concatenated frames (only protein) from
(if we look at number of H-bonds present at same point of time in both).

Because I am not getting the exact match between the two, there is random
difference of 1-3 H-bonds at some point of time.



I suspect that the issue stems from having to manually set the box.  I don't 
understand why you would have to do this after running a simulation in explicit 
solvent.  Did you just extract the protein coordinates from the explicit 
simulation?  If so, I don't see how the box information would be omitted.


You can get spurious H-bonds across PBC if you are manually setting a bad box 
size in a given frame or series of frames.  Without the exact sequence of 
commands from what you have done, it's pure guesswork.


-Justin



On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul  wrote:




On 7/19/13 4:17 AM, bipin singh wrote:


According to the suggestion I added the box to the trajectory using -box
option of trjconv, using the following commands:

trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc

then using the g_hbond on the output trjectory (traj_box.xtc) run
successfully but gives the wrong number of H-bonds between the proteins
atoms.

I have also tried to process the output trajectory (traj_box.xtc) with
trjconv using -pbc mol -ur compact options before using g_hbond, but again
I have got wrong number of H-bonds.

Please help me to rectify the error.



A 0.9-nm cubic box is likely too small to correctly accommodate even an
amino acid, let alone an entire protein.

-Justin



On Fri, Jul 19, 2013 at 11:19 AM, bipin singh 
wrote:

  Thanks a lot Prof. David. I will try this.



On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel <
sp...@xray.bmc.uu.se> wrote:

  On 2013-07-19 06:26, bipin singh wrote:


  Hello all,


I was using g_hbond to calculate H-bonds for a trajectory made from
several
individual snapshots from MD simulation, but because this trajectory
does
not have the coordinates/information for simulation box, g_hbond is
giving
the following error:

Fatal error:
Your computational box has shrunk too much.
g_hbond_mpi can not handle this situation, sorry.


Please let me know, if there is any way to rectify this error.


   you can add a box to your trajectory using trjconv.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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--
*---
Thanks and Regards,
Bipin Singh*







--
==**

Justin A. Lemkul, Ph.D.
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

jalemkul@outerbanks.umaryland.**edu  |
(410) 706-7441

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Justin A. Lemkul, Ph.D.
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

[gmx-users] .n2t file format

[afsaneh maleki]

 Dear gmx users


I scrap lines from some files in oplsaa.ff folder as the following

ffnonbonded file:

[ atomtypes ]

opls_157   CT6 12.01100 0.145   A3.5e-01
2.76144e-01

atomtypes.atp file:

opls_157   12.01100  ; all-atom C: CH3 & CH2, alcohols

also, I looked at /gromacs /Documentation/file format/.n2t that written:

To translate atom names into atom types, the x2top program uses library
files called .n2t files as input. These files contain information about
atom types, charges, and connectivity to neighbors. The format of such a
file is exemplified by:



*C* opls_157  -0.18  12.011  4  H  0.108  H 0.108  H 0.108  C 0.150



The above line interprets an atom named C to be the carbon atom in CH3,
CH2, or alcohols (atom type opls_157).



My question is that carbon atomname with opls_157 atomtype is *C* or CT?

In other word the first column in .n2t is atomneme (CT as mentioned in
ffnonbonded file ) or element name (C as mentioned in file format.n2t )?

Also, are 6, 8 10 columns atomname or element name?



Any help is much appreciated

Afsaneh
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Re: [gmx-users] .n2t file format

[Justin Lemkul]

On 7/19/13 8:20 AM, afsaneh maleki wrote:

  Dear gmx users


I scrap lines from some files in oplsaa.ff folder as the following

ffnonbonded file:

[ atomtypes ]

opls_157   CT6 12.01100 0.145   A3.5e-01
2.76144e-01

atomtypes.atp file:

opls_157   12.01100  ; all-atom C: CH3 & CH2, alcohols

also, I looked at /gromacs /Documentation/file format/.n2t that written:

To translate atom names into atom types, the x2top program uses library
files called .n2t files as input. These files contain information about
atom types, charges, and connectivity to neighbors. The format of such a
file is exemplified by:



*C* opls_157  -0.18  12.011  4  H  0.108  H 0.108  H 0.108  C 0.150



The above line interprets an atom named C to be the carbon atom in CH3,
CH2, or alcohols (atom type opls_157).



My question is that carbon atomname with opls_157 atomtype is *C* or CT?



The type is opls_157 for the purposes of ffnonbonded.itp, which is translated to 
the CT in ffbonded.itp.



In other word the first column in .n2t is atomneme (CT as mentioned in
ffnonbonded file ) or element name (C as mentioned in file format.n2t )?



In Gromacs nomenclature, atom names are whatever is read from the input 
coordinate file (no differentiation between atom name and element name) and atom 
types are force field-specific.



Also, are 6, 8 10 columns atomname or element name?



Both, given Gromacs' interpretation of atom names.  g_x2top will look for 
matches based on whatever element it finds, so in the case of column 6, any of 
these will match: H, HA, H1, H2, etc.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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[gmx-users] Generate topology

[afsaneh maleki]

Dear   Justin

 I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.

The .pdb file is as the following:

ATOM  1  O5  TPT 1  -6.131  -0.245   0.000  0.00

ATOM  2  C21 TPT 1  -5.041   0.384   0.000  0.00

ATOM  3  O6  TPT 1  -5.040   1.814   0.000  0.00

ATOM  4  H12 TPT 1  -5.945   2.134   0.000  0.00

ATOM  5  C18 TPT 1  -3.708  -0.387   0.000  0.00

ATOM  6  C19 TPT 1  -2.374   0.383   0.000  0.00

ATOM  7  H10 TPT 1  -2.373   1.453   0.000  0.00

……

I copied oplsaa.ff folder in my working directory

atomname2type.n2t file is as the following:

O  opls_267   -0.495284   15.9994   1 C 0.1214

C  opls_4700.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214

O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974

H  opls_2700.4173341.0079   1 O 0.0974

C  opls_1450.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387

C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395

H  opls_1460.1108421.0079   1 C 0.1087

……

I used   these command:

] g_x2top  –f  .pdb  –o .top  -pbc –ff oplsaa



But I get:

opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 name to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206



*Fatal error:*

Could only find a forcefield type for 32 out of 44 atoms.





How to solve my problem.

Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I
copyied oplsaa.ff
folder in my working directory. Also I edited  .n2t file in my folder.




Thanks in advance,
Afsaneh
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Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

[Szilárd Páll]

Depending on the level of parallelization (number of nodes and number
of particles/core) you may want to try:

- 2 ranks/node: 8 cores + 1 GPU, no separate PME (default):
  mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0]

- 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separate PME
  mpirun -np 4*Nnodes mdrun_mpi -gpu_id 0011 [-npme 0]

- 4 ranks per node, 2 PP/2PME: 4 cores + 1 GPU (not shared), separate PME
  mpirun -np 4*Nnodes mdrun_mpi [-gpu_id 01] -npme 2*Nnodes

- at high parallelization you may want to try (especially with
homogeneous systems) 8 ranks per node

Cheers,
--
Szilárd


On Fri, Jul 19, 2013 at 4:35 AM, Éric Germaneau  wrote:
> Dear all,
>
> I'm note a gromacs user,  I've installed gromacs 4.6.3 on our cluster and
> making some test.
> Each node of our machine has 16 cores and 2 GPU.
> I'm trying to figure how to submit efficient multiple nodes LSF jobs using
> the maximum of resources.
> After reading the documentation
> 
> on "Acceleration and parallelization" I got confused and inquire some help.
> I'm just wondering whether someone with some experiences on this matter.
> I thank you in advance,
>
> Éric.
>
> --
> /Be the change you wish to see in the world
> / --- Mahatma Gandhi ---
>
> Éric Germaneau 
>
> Shanghai Jiao Tong University
> Network & Information Center
> room 205
> Minhang Campus
> 800 Dongchuan Road
> Shanghai 200240
> China
>
> View Éric Germaneau's profile on LinkedIn
> 
>
> /Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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Re: [gmx-users] Generate topology

[Justin Lemkul]

On 7/19/13 8:53 AM, afsaneh maleki wrote:

Dear   Justin

  I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.

The .pdb file is as the following:

ATOM  1  O5  TPT 1  -6.131  -0.245   0.000  0.00

ATOM  2  C21 TPT 1  -5.041   0.384   0.000  0.00

ATOM  3  O6  TPT 1  -5.040   1.814   0.000  0.00

ATOM  4  H12 TPT 1  -5.945   2.134   0.000  0.00

ATOM  5  C18 TPT 1  -3.708  -0.387   0.000  0.00

ATOM  6  C19 TPT 1  -2.374   0.383   0.000  0.00

ATOM  7  H10 TPT 1  -2.373   1.453   0.000  0.00

……

I copied oplsaa.ff folder in my working directory

atomname2type.n2t file is as the following:

O  opls_267   -0.495284   15.9994   1 C 0.1214

C  opls_4700.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214

O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974

H  opls_2700.4173341.0079   1 O 0.0974

C  opls_1450.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387

C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395

H  opls_1460.1108421.0079   1 C 0.1087

……

I used   these command:

] g_x2top  –f  .pdb  –o .top  -pbc –ff oplsaa



But I get:

opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 name to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206



*Fatal error:*

Could only find a forcefield type for 32 out of 44 atoms.





How to solve my problem.

Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t? I
copyied oplsaa.ff
folder in my working directory. Also I edited  .n2t file in my folder.



Put the .n2t file in the working directory, not in an oplsaa.ff subdirectory.

-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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[gmx-users] Generate topology

[afsaneh maleki]

Dear Justin
thanks for your reply,

I did it. when I put the .n2t in my working directory,I have gotten this
error.

thanks in advance,
Afsaneh
-- 
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Re: [gmx-users] Generate topology

[Justin Lemkul]

On 7/19/13 9:10 AM, afsaneh maleki wrote:

Dear Justin
thanks for your reply,

I did it. when I put the .n2t in my working directory,I have gotten this
error.



What error?

-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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[gmx-users] Generate topology -2

[afsaneh maleki]

Dear  Justin



I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.

The .pdb file is as the following:

ATOM  1  O5  TPT 1  -6.131  -0.245   0.000  0.00

ATOM  2  C21 TPT 1  -5.041   0.384   0.000  0.00

ATOM  3  O6  TPT 1  -5.040   1.814   0.000  0.00

ATOM  4  H12 TPT 1  -5.945   2.134   0.000  0.00

ATOM  5  C18 TPT 1  -3.708  -0.387   0.000  0.00

ATOM  6  C19 TPT 1  -2.374   0.383   0.000  0.00

ATOM  7  H10 TPT 1  -2.373   1.453   0.000  0.00

……

I edited atomname2type.n2t file is as the following:

O  opls_267   -0.495284   15.9994   1 C 0.1214

C  opls_4700.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214

O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974

H  opls_2700.4173341.0079   1 O 0.0974

C  opls_1450.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387

C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395

H  opls_1460.1108421.0079   1 C 0.1087

……

I used   these command:

] g_x2top  –f  .pdb  –o  .top  -pbc –ff oplsaa



And gromacs get me:



opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206

Fatal error:

Could only find a forcefield type for 32 out of 44 atoms for more
information and tips for troubleshooting,

………..



I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as the above mentioned in my working
directory.



How to solve my problem?

Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t?



 Thanks in advance,

Afsaneh
--
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Re: [gmx-users] Generate topology -2

[Justin Lemkul]

On 7/19/13 9:32 AM, afsaneh maleki wrote:

Dear  Justin



I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.

The .pdb file is as the following:

ATOM  1  O5  TPT 1  -6.131  -0.245   0.000  0.00

ATOM  2  C21 TPT 1  -5.041   0.384   0.000  0.00

ATOM  3  O6  TPT 1  -5.040   1.814   0.000  0.00

ATOM  4  H12 TPT 1  -5.945   2.134   0.000  0.00

ATOM  5  C18 TPT 1  -3.708  -0.387   0.000  0.00

ATOM  6  C19 TPT 1  -2.374   0.383   0.000  0.00

ATOM  7  H10 TPT 1  -2.373   1.453   0.000  0.00

……

I edited atomname2type.n2t file is as the following:

O  opls_267   -0.495284   15.9994   1 C 0.1214

C  opls_4700.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214

O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974

H  opls_2700.4173341.0079   1 O 0.0974

C  opls_1450.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387

C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395

H  opls_1460.1108421.0079   1 C 0.1087

……

I used   these command:

] g_x2top  –f  .pdb  –o  .top  -pbc –ff oplsaa



And gromacs get me:



opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206

Fatal error:

Could only find a forcefield type for 32 out of 44 atoms for more
information and tips for troubleshooting,

………..



I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as the above mentioned in my working
directory.



How to solve my problem?

Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t?



Let's not go backwards.  I responded to this post already and you gave a cryptic 
reply about some new error.  Please respond to the other post.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
--
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Re: [gmx-users] Generate topology

[afsaneh maleki]

Dear Justin

I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.

I used   these command:

] g_x2top  –f  .pdb  –o  .top  -pbc –ff oplsaa



And gromacs get me:



opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206

Fatal error:

Could only find a forcefield type for 32 out of 44 atoms

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

website at http://www.gromacs.org/Documentation/Errors
………..
I seem can't read atomname2type.n2t file from my working directory.

Thanks very much.
Afsaneh
On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul  wrote:

>
>
> On 7/19/13 8:53 AM, afsaneh maleki wrote:
>
>>  Dear   Justin
>>
>>   I want a topology for an arbitrary molecule (44 atom) and I use x2top
>> program that .n2t file is it’s input.
>>
>> The .pdb file is as the following:
>>
>> ATOM  1  O5  TPT 1  -6.131  -0.245   0.000  0.00
>>
>> ATOM  2  C21 TPT 1  -5.041   0.384   0.000  0.00
>>
>> ATOM  3  O6  TPT 1  -5.040   1.814   0.000  0.00
>>
>> ATOM  4  H12 TPT 1  -5.945   2.134   0.000  0.00
>>
>> ATOM  5  C18 TPT 1  -3.708  -0.387   0.000  0.00
>>
>> ATOM  6  C19 TPT 1  -2.374   0.383   0.000  0.00
>>
>> ATOM  7  H10 TPT 1  -2.373   1.453   0.000  0.00
>>
>> ……
>>
>> I copied oplsaa.ff folder in my working directory
>>
>> atomname2type.n2t file is as the following:
>>
>> O  opls_267   -0.495284   15.9994   1 C 0.1214
>>
>> C  opls_4700.594326   12.0110   3 C 0.1487  O  0.1306   O  0.1214
>>
>> O  opls_268   -0.560735   15.9994   2 C 0.1306  H  0.0974
>>
>> H  opls_2700.4173341.0079   1 O 0.0974
>>
>> C  opls_1450.037549   12.0110   3 C 0.1487  C 0.1387  C 0.1387
>>
>> C  opls_145   -0.145422   12.0110   3 C 0.1387  H 0.1087 C 0.1395
>>
>> H  opls_1460.1108421.0079   1 C 0.1087
>>
>> ……
>>
>> I used   these command:
>>
>> ] g_x2top  –f  .pdb  –o .top  -pbc –ff oplsaa
>>
>>
>>
>> But I get:
>>
>> opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t
>>
>> There are 23 name to type translations in file oplsaa.ff
>>
>> Generating bonds from distances...
>>
>> atom 44
>>
>> Can not find forcefield for atom C21-2 with 3 bonds
>>
>> Can not find forcefield for atom C18-5 with 3 bonds
>>
>> Can not find forcefield for atom C16-10 with 3 bonds
>>
>> Can not find forcefield for atom C20-11 with 3 bonds
>>
>> Can not find forcefield for atom C15-17 with 3 bonds
>>
>> Can not find forcefield for atom C12-18 with 3 bonds
>>
>> Can not find forcefield for atom C7-27 with 3 bonds
>>
>> Can not find forcefield for atom C5-28 with 3 bonds
>>
>> Can not find forcefield for atom C3-33 with 3 bonds
>>
>> Can not find forcefield for atom C2-34 with 3 bonds
>>
>> Can not find forcefield for atom C9-40 with 3 bonds
>>
>> Can not find forcefield for atom C10-41 with 3 bonds
>>
>>
>>
>> Program g_x2top, VERSION 4.5.4
>>
>> Source code file: g_x2top.c, line: 206
>>
>>
>>
>> *Fatal error:*
>>
>>
>> Could only find a forcefield type for 32 out of 44 atoms.
>>
>>
>>
>>
>>
>> How to solve my problem.
>>
>> Why do gromacs open /
>> usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I
>> copyied oplsaa.ff
>> folder in my working directory. Also I edited  .n2t file in my folder.
>>
>>
> Put the .n2t file in the working directory, not in an oplsaa.ff
> subdirectory.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> 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
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at 

Re: [gmx-users] Generate topology

[Justin Lemkul]

On 7/19/13 10:06 AM, afsaneh maleki wrote:

Dear Justin

I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.

I used   these command:

] g_x2top  –f  .pdb  –o  .top  -pbc –ff oplsaa



And gromacs get me:



opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t

There are 23 names to type translations in file oplsaa.ff

Generating bonds from distances...

atom 44

Can not find forcefield for atom C21-2 with 3 bonds

Can not find forcefield for atom C18-5 with 3 bonds

Can not find forcefield for atom C16-10 with 3 bonds

Can not find forcefield for atom C20-11 with 3 bonds

Can not find forcefield for atom C15-17 with 3 bonds

Can not find forcefield for atom C12-18 with 3 bonds

Can not find forcefield for atom C7-27 with 3 bonds

Can not find forcefield for atom C5-28 with 3 bonds

Can not find forcefield for atom C3-33 with 3 bonds

Can not find forcefield for atom C2-34 with 3 bonds

Can not find forcefield for atom C9-40 with 3 bonds

Can not find forcefield for atom C10-41 with 3 bonds



Program g_x2top, VERSION 4.5.4

Source code file: g_x2top.c, line: 206

Fatal error:

Could only find a forcefield type for 32 out of 44 atoms

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

website at http://www.gromacs.org/Documentation/Errors
………..
I seem can't read atomname2type.n2t file from my working directory.



Use "-ff select" to choose the force field that resides in the working 
directory.  Specifying "-ff oplsaa" tells g_x2top to use the oplsaa.ff directory 
in $GMXLIB.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

[gigo]

Hi!

On 2013-07-17 21:08, Mark Abraham wrote:

You tried ppn3 (with and without --loadbalance)?


I was testing on 8-replicas simulation.

1) Without --loadbalance and -np 8.
Excerpts from the script:
#PBS -l nodes=8:ppn=3
setenv OMP_NUM_THREADS 4
mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -replex 2500 -cpi -pin 
on


Excerpts from logs:
Using 3 MPI processes
Using 4 OpenMP threads per MPI process
(...)
Overriding thread affinity set outside mdrun_mpi

Pinning threads with an auto-selected logical core stride of 1

WARNING: In MPI process #0: Affinity setting for 1/4 threads failed.
 This can cause performance degradation! If you think your 
setting are

 correct, contact the GROMACS developers.


WARNING: In MPI process #2: Affinity setting for 4/4 threads failed.

Load: The job was allocated 24 cores (3 cores on 8 different nodes). 
Each OpenMP thread uses ~1/3 of a CPU core on average.
Conclusions: MPI runs as many processes as cores requested 
(nnodes*ppn=24), it ignores OMP_NUM_THREADS env ==> this is wrong and is 
not Gromacs issue. Each MPI process forks to 4 threads as requested. The 
24-core limit granted by Torque is not violated.


2) The same script, but with -np 8, to limit the number of MPI 
processes to the number of replicas

Logs:
Using 1 MPI process
Using 4 OpenMP threads
(...)

Replicas 0,3 and 6: WARNING: Affinity setting for 1/4 threads failed.
Replicas 1,2,4,5,7: WARNING: Affinity setting for 4/4 threads failed.


Load: The job was allocated 24 cores on 8 nodes. Only on first 3 nodes 
mpiexec was run. Each OpenMP thread uses ~20% of a CPU core.


3) -np 8 --loadbalance
Excerpts from logs:
Using 1 MPI process
Using 4 OpenMP threads
(...)
Each replica says: WARNING: Affinity setting for 3/4 threads failed.

Load: MPI processes spread evenly on all 8 nodes. Each OpenMP thread 
uses ~50% of a CPU core.


4) -np 8 --loadbalance, #PBS -l nodes=8:ppn=4 <== this worked ~OK with 
gromacs 4.6.2

Logs:
WARNING: Affinity setting for 2/4 threads failed.

Load: 32 cores allocated on 8 nodes. MPI processes spread evenly, each 
OpenMP thread uses ~70% of a CPU core.
With 144 replicas the simulation did not produce any results, just got 
stuck.



Some thoughts: the main problem is most probably in the way MPI 
interprets the information from torque, it is not Gromacs related. MPI 
ignores OMP_NUM_THREADS. The environment is just broken. Since 
gromacs-4.6.2 behaved better than 4.6.3 there, I am coming back to it.

Best,
G



Mark

On Wed, Jul 17, 2013 at 6:30 PM, gigo  wrote:

On 2013-07-13 11:10, Mark Abraham wrote:


On Sat, Jul 13, 2013 at 1:24 AM, gigo  wrote:


On 2013-07-12 20:00, Mark Abraham wrote:



On Fri, Jul 12, 2013 at 4:27 PM, gigo  wrote:



Hi!

On 2013-07-12 11:15, Mark Abraham wrote:




What does --loadbalance do?





It balances the total number of processes across all allocated 
nodes.




OK, but using it means you are hostage to its assumptions about 
balance.




Thats true, but as long as I do not try to use more resources that 
the
torque gives me, everything is OK. The question is, what is a 
proper way

of
running multiple simulations in parallel with MPI that are further
parallelized with OpenMP, when pinning fails? I could not find any 
other.



I think pinning fails because you are double-crossing yourself. You 
do

not want 12 MPI processes per node, and that is likely what ppn is
setting. AFAIK your setup should work, but I haven't tested it.




The
thing is that mpiexec does not know that I want each replica to 
fork to

4
OpenMP threads. Thus, without this option and without affinities 
(in a

sec
about it) mpiexec starts too many replicas on some nodes - 
gromacs

complains
about the overload then - while some cores on other nodes are not 
used.

It
is possible to run my simulation like that:

mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi 
(without

--loadbalance for mpiexec and without -ntomp for mdrun)

Then each replica runs on 4 MPI processes (I allocate 4 times 
more

cores
then replicas and mdrun sees it). The problem is that it is much 
slower

than
using OpenMP for each replica. I did not find any other way than
--loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to 
use

MPI
and OpenMP at the same time on the torque-controlled cluster.




That seems highly surprising. I have not yet encountered a job
scheduler that was completely lacking a "do what I tell you" 
layout
scheme. More importantly, why are you using #PBS -l 
nodes=48:ppn=12?




I thing that torque is very similar to all PBS-like resource 
managers in
this regard. It actually does what I tell it to do. There are 
12-core

nodes,
I ask for 48 of them - I get them (simple #PBS -l ncpus=576 does 
not

work),
end of story. Now, the program that I run is responsible for 
populating

resources that I got.



No, that's not the end of the story. The scheduler and the MPI 
system
typically cooperate to populate the MPI processes on the hardware, 
set
OMP