[gmx-users] g_select error

[Albert]

hello:

 I am trying to use g_select to make an index file with command:


g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx

but it failed with messages:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

Assertion failed for g in file 
/home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel

dump core ? (y/n)


thank you very much
Albert
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Re: [gmx-users] how to indicate solvent flexibility?

[Albert]

Hello Justin and Leandro:

  thanks a lot for kind advices. I am trying to us the g_msd to 
calculate the density:


first I made a index file called density.ndx with g_select, defined the 
solvent within 6A of a residue


after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o 
msd.xvg


a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements


I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, 
line: 739


Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Can't You Make This Thing Go Faster ? (Black Crowes)


thank you very much
Albert





On 01/08/2013 06:15 PM, Justin Lemkul wrote:



On 1/8/13 11:42 AM, Albert wrote:

hello:

   I've finished a 60ns MD simulation with Gromacs and I found that the
flixbility of solvent molecules inside the protein is different when 
it binds
with different ligands: ie. in one case the solvent can move very 
fast with bulk
environment, and in other case the solvent forms type Hbonds with 
resdiues
inside protein.  I am just wondering how which module of Gromacs can 
I use to
indicate the solvent difference in flexibility? Is it possible to 
calculate the

entropy in certain region (let's say: 20Z30 ) of the solvent?



It sounds like g_rmsf and g_msd may be useful here.  The only way to 
specify geometric criteria for index groups is to use g_select, but 
then the analysis has to be done on each individual frame, not the 
trajectory.  Dynamic selections will be more conveniently implemented 
in a future Gromacs version.


-Justin



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Re: [gmx-users] how to indicate solvent flexibility?

[David van der Spoel]

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.



first I made a index file called density.ndx with g_select, defined the
solvent within 6A of a residue

after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o
msd.xvg

a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements


I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c,
line: 739

Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Can't You Make This Thing Go Faster ? (Black Crowes)


thank you very much
Albert





On 01/08/2013 06:15 PM, Justin Lemkul wrote:



On 1/8/13 11:42 AM, Albert wrote:

hello:

   I've finished a 60ns MD simulation with Gromacs and I found that the
flixbility of solvent molecules inside the protein is different when
it binds
with different ligands: ie. in one case the solvent can move very
fast with bulk
environment, and in other case the solvent forms type Hbonds with
resdiues
inside protein.  I am just wondering how which module of Gromacs can
I use to
indicate the solvent difference in flexibility? Is it possible to
calculate the
entropy in certain region (let's say: 20Z30 ) of the solvent?



It sounds like g_rmsf and g_msd may be useful here.  The only way to
specify geometric criteria for index groups is to use g_select, but
then the analysis has to be done on each individual frame, not the
trajectory.  Dynamic selections will be more conveniently implemented
in a future Gromacs version.

-Justin






--
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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[gmx-users] Reordering of a large GRO file - how

[Jernej Zidar]

Hi.
  I used editconf to replicate a small lipid bilayer patch, after
editing the topology file I'm able to simulate it. I have one small
question/issue.

  I would like to use g_membed to add a large molecule into the water
section (SOL) but editconf operates in such a way that it just
replicates the initial system, thus my SOL section is not continuous
but is scattered all over the GRO file hence the command fails.

  Is there a smart way to reorder so the SOL section would be
continuous*? How does GROMPP parse the GRO file?

  The topology file now looks like this:
A 34345
B 25
SOL 1
A 34345
B 25
SOL 1
...

Thanks in advance,
Jernej Zidar
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Re: [gmx-users] how to indicate solvent flexibility?

[Albert]

On 01/10/2013 11:14 AM, David van der Spoel wrote:

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.


that's strange. Here is the information which I think it is what I want.


g_msd -h


DESCRIPTION
---
g_msd computes the mean square displacement (MSD) of atoms from a set of
initial positions. This provides an easy way to compute the diffusion
constant using the Einstein relation. The time between the reference points
for the MSD calculation is set with -trestart. The diffusion constant is
calculated by least squares fitting a straight line (D*t + c) through the
MSD(t) from -beginfit to -endfit (note that t is time from the reference
positions, not simulation time). An error estimate given, which is the
difference of the diffusion coefficients obtained from fits over the two
halves of the fit interval.

There are three, mutually exclusive, options to determine different types of
mean square displacement: -type, -lateral and -ten. Option -ten writes the
full MSD tensor for each group, the order in the output is: trace xx yy 
zz yx

zx zy.

If -mol is set, g_msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules.

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[gmx-users] Gromacs 4.6 turn off ecc

[sebastian]

Dear Gromacs user,

is there a way to manually  turn off ECC (gromacs version 4.6)?

Thanks
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Re: [gmx-users] g_select error

[Justin Lemkul]

On 1/10/13 4:08 AM, Albert wrote:

hello:

  I am trying to use g_select to make an index file with command:


g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx

but it failed with messages:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
  based on residue and atom names, since they could not be
  definitively assigned from the information in your input
  files. These guessed numbers might deviate from the mass
  and radius of the atom type. Please check the output
  files if necessary.

Assertion failed for g in file
/home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel
dump core ? (y/n)



Apparently whatever you're tying to select requires a .tpr file as input to work 
rather than a .pdb file.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] necessity of energy minimization

[Justin Lemkul]

On 1/10/13 2:32 AM, Gmx Niki wrote:

Hi All,

when I run energy minimization the system gives error, and broke up. it has error about 
steep integrator and says tha: steepest time is too small.


It's always better to post the full message you get, rather than leaving us 
guessing what you're dealing with.  In this case, I'm assuming what you're 
seeing is 
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision, 
which is not actually an error.  I don't know what you mean by broke up, but 
maybe PBC effects explain it.



but the system is running by MD integrator without any em step). is the energy 
minimization necessary to all cases? for example in DL_POL software we dont 
have  enegy minimization , seperately. is it correct that I start simulation 
steps by md integrator and NVT ensemble?



EM is always recommended.  In the majority of cases, if you try to go straight 
into dynamics, the system will explode due to high forces.  You might get lucky 
and not need it, but that would be extremely uncommon.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] Reordering of a large GRO file - how

[Justin Lemkul]

On 1/10/13 4:50 AM, Jernej Zidar wrote:

Hi.
   I used editconf to replicate a small lipid bilayer patch, after
editing the topology file I'm able to simulate it. I have one small
question/issue.

   I would like to use g_membed to add a large molecule into the water
section (SOL) but editconf operates in such a way that it just
replicates the initial system, thus my SOL section is not continuous
but is scattered all over the GRO file hence the command fails.

   Is there a smart way to reorder so the SOL section would be
continuous*? How does GROMPP parse the GRO file?



Use grep and rebuild the coordinate file with cat.  grompp simply reads through 
the file and matches the contents of the coordinate and topology files in order 
to map all the necessary parameters to the corresponding atoms.


-Justin


   The topology file now looks like this:
A 34345
B 25
SOL 1
A 34345
B 25
SOL 1
...

Thanks in advance,
Jernej Zidar



--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/10/13 5:21 AM, Albert wrote:

On 01/10/2013 11:14 AM, David van der Spoel wrote:

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.


that's strange. Here is the information which I think it is what I want.



David's point was that g_msd does not calculate density, which you stated was 
what you were trying to do.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/10/13 4:45 AM, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to calculate the
density:

first I made a index file called density.ndx with g_select, defined the solvent
within 6A of a residue

after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o msd.xvg

a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements



Each of these groups corresponds to the atoms that satisfied the g_select 
criteria for a given frame.  That may not continuously apply to what you 
actually want to measure.




I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, line: 739

Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



So make an index file that contains intact molecules.  That's a prerequisite for 
using the -mol flag.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] Gromacs 4.6 turn off ecc

[Justin Lemkul]

On 1/10/13 5:43 AM, sebastian wrote:

Dear Gromacs user,

is there a way to manually  turn off ECC (gromacs version 4.6)?



That's outside of Gromacs.  Google has lots to say...

http://nvidia.helpmax.net/en/workstation/ecc-state-control/how-do-i/turn-my-gpu-ecc-on-or-off/

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Compute the end to end distance distribution for surfactant

[ABEL Stephane 175950]

Dear All, 

I would like to compute the end to end distribution for different parts (i.e.  
hydrophobic and the polar) of several detergent molecules. I know that 
g_polystat can do the job and indeed i can obtain the end-to-end distance of 
the whole  molecule (at least for  the distance vs. time). But it is not clear 
to me how to obtain the end to end distance values for the different parts of 
my molecule with g_polystat. 

Can you help me ?

Stephane

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Re: [gmx-users] Compute the end to end distance distribution for surfactant

[Justin Lemkul]

On 1/10/13 6:38 AM, ABEL Stephane 175950 wrote:

Dear All,

I would like to compute the end to end distribution for different parts (i.e.  
hydrophobic and the polar) of several detergent molecules. I know that 
g_polystat can do the job and indeed i can obtain the end-to-end distance of 
the whole  molecule (at least for  the distance vs. time). But it is not clear 
to me how to obtain the end to end distance values for the different parts of 
my molecule with g_polystat.



g_polystat -h includes:

The end-to-end distance is then determined using the first and the
last atom in the index group for each molecules.

As with nearly all Gromacs programs, you can give it an index file of whatever 
subset of atoms you want.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Reordering of a large GRO file - how

[Jernej Zidar]

So the residue numbers don't matter? They will be renumbered accordingly after 
I reassemble the GRO file. That's neat!

Thanks,
Jernej

On 10. jan. 2013, at 19:29, gmx-users-requ...@gromacs.org wrote:

 Subject: Re: [gmx-users] Reordering of a large GRO file - how
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 50eea589.4030...@vt.edu
 Content-Type: text/plain; charset=UTF-8; format=flowed
 
 
 
 On 1/10/13 4:50 AM, Jernej Zidar wrote:
 Hi.
   I used editconf to replicate a small lipid bilayer patch, after
 editing the topology file I'm able to simulate it. I have one small
 question/issue.
 
   I would like to use g_membed to add a large molecule into the water
 section (SOL) but editconf operates in such a way that it just
 replicates the initial system, thus my SOL section is not continuous
 but is scattered all over the GRO file hence the command fails.
 
   Is there a smart way to reorder so the SOL section would be
 continuous*? How does GROMPP parse the GRO file?
 
 
 Use grep and rebuild the coordinate file with cat.  grompp simply reads 
 through 
 the file and matches the contents of the coordinate and topology files in 
 order 
 to map all the necessary parameters to the corresponding atoms.

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Re: [gmx-users] Reordering of a large GRO file - how

[Justin Lemkul]

On 1/10/13 7:00 AM, Jernej Zidar wrote:

So the residue numbers don't matter? They will be renumbered accordingly after 
I reassemble the GRO file. That's neat!



grompp won't do that.  genconf -renumber will.  If you need an index file, make 
sure to create it from a suitably numbered file after it's been rearranged.


-Justin


Thanks,
Jernej

On 10. jan. 2013, at 19:29, gmx-users-requ...@gromacs.org wrote:


Subject: Re: [gmx-users] Reordering of a large GRO file - how
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 50eea589.4030...@vt.edu
Content-Type: text/plain; charset=UTF-8; format=flowed



On 1/10/13 4:50 AM, Jernej Zidar wrote:

Hi.
   I used editconf to replicate a small lipid bilayer patch, after
editing the topology file I'm able to simulate it. I have one small
question/issue.

   I would like to use g_membed to add a large molecule into the water
section (SOL) but editconf operates in such a way that it just
replicates the initial system, thus my SOL section is not continuous
but is scattered all over the GRO file hence the command fails.

   Is there a smart way to reorder so the SOL section would be
continuous*? How does GROMPP parse the GRO file?



Use grep and rebuild the coordinate file with cat.  grompp simply reads through
the file and matches the contents of the coordinate and topology files in order
to map all the necessary parameters to the corresponding atoms.






--


Justin A. Lemkul, Ph.D.
Research Scientist
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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RE: [gmx-users] Gromacs + Mopac error

[raul arias]

Hi Javier,
Thanks for your answer.
I apologize for the delay in responding, but it's better with orca compiled 
version.
Now I'm trying to compile with mopac again, but I think that my mistake is how 
to compile mopac. 
I'm following the steps of:
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM


But in the version mopac7-1.11 has a subdirectory called fortran where the 
codes are. 
Also, here mopac.f file does not exist, but if the file mopac7app.f (I have to 
delete this? Like as deriv.f and moldat.f files)
Can you help me at that point?


 From: j...@um.es
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Gromacs + Mopac error
 Date: Tue, 8 Jan 2013 08:59:31 +
 
 Hi
 
 The problem is that in your first try the gaussian interface is being 
 used, while in the second the orca interface is used.
 
 The first try should have used the mopac interface but it apparently 
 ignored it, the reason why must be written in the configure output. 
 Could you show the last lines of such output? or clean the installation 
 directory and try again configure (using the options you mentioned 
 first, or you can add both --withoiut-qmmm-gaussian --with-qmmm-mopac) + 
 make + make install and provide the last lines of each output?
 
 Javier
 
 El 07/01/13 19:03, raul arias escribió:
  I'm trying to compile Gromacs with mopac using the instructions in the 
  tutorial
  (the compilation of mopac was made with gfortran since f77 gave me error)
 
  ./configure --prefix=/home/raul/gromacs_mopac LIBS=-lmopac 
  LDFLAGS=-L/home/raul/fftw/lib -L/home/raul/lib CPPFLAGS=-DUSE_MOPAC 
  -I/home/raul/fftw/include --enable-mpi --disable-float --with-fft=fftw3 
  --with-qmmm-mopac
 
  everything is gone fine, but when I tried to run my simulation AM1, gave me 
  this error:
 
  starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
  5000 steps,  5.0 ps.
  nr mm atoms in gaussian.c = 3027
  Calling '(null)/(null)  input.com  input.log'
  sh: 1: Syntax error: word unexpected
  ---
  Program mdrun_d, VERSION 4.5.5
  Source code file: qm_gaussian.c, line: 913
  Fatal error:
  Call to '(null)/(null)  input.com  input.log' failed
 
 
  when I try to compile with the option: --without-qmmm-gaussian
  The error change to:
 
  starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
  5000 steps,  5.0 ps.
  No information on the calculation given in (null).ORCAINFO
  ---
  Program mdrun_d, VERSION 4.5.5
  Source code file: qm_orca.c, line: 144
 
  Routine should not have been called:
  qm_orca.c
 
 
  Any suggestions for my problem!
 
  Thank you.
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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 -- 
 Javier CEREZO BASTIDA
 Ph.D. Student
 Physical Chemistry
 Universidad de Murcia
 30100, Murcia (SPAIN)
 T: (0034)868887434
 
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 gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Gromacs + Mopac error

[Javier Cerezo]

Hi Raul

I'd need to see the exact errors you get to be able to help you, and 
other info such as which OS and compilers are you using. From your 
previous post, it seemed that the mopac interface was not being compiled 
with gromacs, but gaussian or orca ones were, according to the errors 
you showed (note they mention gaussian.c and qm_orca.c)


The steps in the gromacs web should work (note you have to change some 
files), and if not you can also try the precompiled library (libmopac.a, 
in the same page). If you want to compile it by yourself, you can get 
MOPAC code from http://openmopac.net/Downloads/Downloads.html (select 
MOPAC7). Still, there might be some issues when compiling libmopac or in 
runtime, but in such a case, we'd need to see what actual 
errors/warnings are you observing (in your last mail it looked like the 
installation went perfectly).


Additionally, in case it could be of some help, I reported a 
installation of gromacs-mopac in this mailing list some time ago

http://lists.gromacs.org/pipermail/gmx-users/2011-November/066133.html

Try all that and report back if you encounter any problem

Javier


El 10/01/13 14:59, raul arias escribió:

Hi Javier,
Thanks for your answer.
I apologize for the delay in responding, but it's better with orca compiled 
version.
Now I'm trying to compile with mopac again, but I think that my mistake is how 
to compile mopac.
I'm following the steps of:
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM


But in the version mopac7-1.11 has a subdirectory called fortran where the 
codes are.
Also, here mopac.f file does not exist, but if the file mopac7app.f (I have to 
delete this? Like as deriv.f and moldat.f files)
Can you help me at that point?



From: j...@um.es
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Gromacs + Mopac error
Date: Tue, 8 Jan 2013 08:59:31 +

Hi

The problem is that in your first try the gaussian interface is being
used, while in the second the orca interface is used.

The first try should have used the mopac interface but it apparently
ignored it, the reason why must be written in the configure output.
Could you show the last lines of such output? or clean the installation
directory and try again configure (using the options you mentioned
first, or you can add both --withoiut-qmmm-gaussian --with-qmmm-mopac) +
make + make install and provide the last lines of each output?

Javier

El 07/01/13 19:03, raul arias escribió:

I'm trying to compile Gromacs with mopac using the instructions in the tutorial
(the compilation of mopac was made with gfortran since f77 gave me error)

./configure --prefix=/home/raul/gromacs_mopac LIBS=-lmopac LDFLAGS=-L/home/raul/fftw/lib 
-L/home/raul/lib CPPFLAGS=-DUSE_MOPAC -I/home/raul/fftw/include --enable-mpi 
--disable-float --with-fft=fftw3 --with-qmmm-mopac

everything is gone fine, but when I tried to run my simulation AM1, gave me 
this error:

starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
5000 steps,  5.0 ps.
nr mm atoms in gaussian.c = 3027
Calling '(null)/(null)  input.com  input.log'
sh: 1: Syntax error: word unexpected
---
Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913
Fatal error:
Call to '(null)/(null)  input.com  input.log' failed


when I try to compile with the option: --without-qmmm-gaussian
The error change to:

starting mdrun 'PHOTOACTIVE YELLOW PROTEIN'
5000 steps,  5.0 ps.
No information on the calculation given in (null).ORCAINFO
---
Program mdrun_d, VERSION 4.5.5
Source code file: qm_orca.c, line: 144

Routine should not have been called:
qm_orca.c


Any suggestions for my problem!

Thank you.
  --
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--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434

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Re: [gmx-users] cann't calculate a silver particle

[Justin Lemkul]

On 1/10/13 6:14 AM, Alexej Mazheika wrote:

Hi all!

I am new in MD and in Gromacs. I try to calculate the structure of an Ag125
particle in the gas phase. But during the optimization, all silver atoms
fly apart around the cell. So no cluster exists at the end even by
relatively low temperatures. The constants for LJ potential I took from
experimental data. I guess that something can be wrong in the grompp.mdp,
which I took from examples in share/tutor/ and modified a bit, but I cann't
understand what's the matter. Input files are shown below

Alex

*conf.gro:*

Bulk silver, t = 0.0
   125
  0001Clust   Ag1   0.000   0.000   0.000
  0002Clust   Ag2   0.204   0.204   0.000
  0003Clust   Ag3   0.409   0.409   0.000
  0004Clust   Ag4  -0.409  -0.409   0.000
  0005Clust   Ag5  -0.204  -0.204   0.000
  0006Clust   Ag6   0.204   0.000   0.204
  0007Clust   Ag7   0.409   0.204   0.204
  0008Clust   Ag8   0.613   0.409   0.204
  0009Clust   Ag9  -0.204  -0.409   0.204
  0010Clust   Ag   10   0.000  -0.204   0.204
  0011Clust   Ag   11   0.409   0.000   0.409
  0012Clust   Ag   12   0.613   0.204   0.409
  0013Clust   Ag   13   0.817   0.409   0.409
  0014Clust   Ag   14   0.000  -0.409   0.409
  0015Clust   Ag   15   0.204  -0.204   0.409
  0016Clust   Ag   16  -0.409   0.000  -0.409
  0017Clust   Ag   17  -0.204   0.204  -0.409
  0018Clust   Ag   18   0.000   0.409  -0.409
  0019Clust   Ag   19  -0.817  -0.409  -0.409
  0020Clust   Ag   20  -0.613  -0.204  -0.409
  0021Clust   Ag   21  -0.204   0.000  -0.204
  0022Clust   Ag   22   0.000   0.204  -0.204
  0023Clust   Ag   23   0.204   0.409  -0.204
  0024Clust   Ag   24  -0.613  -0.409  -0.204
  0025Clust   Ag   25  -0.409  -0.204  -0.204
  0026Clust   Ag   26   0.000   0.204   0.204
  0027Clust   Ag   27   0.204   0.409   0.204
  0028Clust   Ag   28   0.409   0.613   0.204
  0029Clust   Ag   29  -0.409  -0.204   0.204
  0030Clust   Ag   30  -0.204   0.000   0.204
  0031Clust   Ag   31   0.204   0.204   0.409
  0032Clust   Ag   32   0.409   0.409   0.409
  0033Clust   Ag   33   0.613   0.613   0.409
  0034Clust   Ag   34  -0.204  -0.204   0.409
  0035Clust   Ag   35   0.000   0.000   0.409
  0036Clust   Ag   36   0.409   0.204   0.613
  0037Clust   Ag   37   0.613   0.409   0.613
  0038Clust   Ag   38   0.817   0.613   0.613
  0039Clust   Ag   39   0.000  -0.204   0.613
  0040Clust   Ag   40   0.204   0.000   0.613
  0041Clust   Ag   41  -0.409   0.204  -0.204
  0042Clust   Ag   42  -0.204   0.409  -0.204
  0043Clust   Ag   43   0.000   0.613  -0.204
  0044Clust   Ag   44  -0.817  -0.204  -0.204
  0045Clust   Ag   45  -0.613   0.000  -0.204
  0046Clust   Ag   46  -0.204   0.204   0.000
  0047Clust   Ag   47   0.000   0.409   0.000
  0048Clust   Ag   48   0.204   0.613   0.000
  0049Clust   Ag   49  -0.613  -0.204   0.000
  0050Clust   Ag   50  -0.409   0.000   0.000
  0051Clust   Ag   51   0.000   0.409   0.409
  0052Clust   Ag   52   0.204   0.613   0.409
  0053Clust   Ag   53   0.409   0.817   0.409
  0054Clust   Ag   54  -0.409   0.000   0.409
  0055Clust   Ag   55  -0.204   0.204   0.409
  0056Clust   Ag   56   0.204   0.409   0.613
  0057Clust   Ag   57   0.409   0.613   0.613
  0058Clust   Ag   58   0.613   0.817   0.613
  0059Clust   Ag   59  -0.204   0.000   0.613
  0060Clust   Ag   60   0.000   0.204   0.613
  0061Clust   Ag   61   0.409   0.409   0.817
  0062Clust   Ag   62   0.613   0.613   0.817
  0063Clust   Ag   63   0.817   0.817   0.817
  0064Clust   Ag   64   0.000   0.000   0.817
  0065Clust   Ag   65   0.204   0.204   0.817
  0066Clust   Ag   66  -0.409   0.409   0.000
  0067Clust   Ag   67  -0.204   0.613   0.000
  0068Clust   Ag   68   0.000   0.817   0.000
  0069Clust   Ag   69  -0.817   0.000   0.000
  0070Clust   Ag   70  -0.613   0.204   0.000
  0071Clust   Ag   71  -0.204   0.409   0.204
  0072Clust   Ag   72   0.000   0.613   0.204
  0073Clust   Ag   73   0.204   0.817   0.204
  0074Clust   Ag   74  -0.613   0.000   0.204
  0075Clust   Ag   75  -0.409   0.204   0.204
  0076Clust   Ag   76   0.000  -0.409  -0.409
  0077Clust   Ag   77   0.204  -0.204  -0.409
  0078Clust   Ag   78   0.409   0.000  -0.409
  0079Clust   Ag   79  -0.409  -0.817  -0.409
  0080Clust   Ag   80  -0.204  -0.613  -0.409
  0081Clust   Ag   81   0.204  -0.409  -0.204
  0082Clust   Ag   82   0.409  -0.204  -0.204
  0083Clust   Ag   83   0.613   0.000  -0.204
  0084Clust   Ag   84  -0.204  -0.817  -0.204
  0085Clust   Ag   85   0.000  -0.613  -0.204
  0086Clust   Ag   86   0.409  -0.409   0.000
  0087Clust   Ag   87   0.613  -0.204   0.000
  0088Clust   Ag   88   0.817   0.000   0.000
  0089Clust   Ag   89   0.000  -0.817   0.000
  0090Clust   Ag   90   0.204  -0.613   0.000
  0091Clust   Ag   91  -0.409  -0.409  -0.817
  0092Clust   Ag   92  -0.204  -0.204  -0.817
  0093Clust   Ag   93   0.000   0.000  -0.817
  0094Clust   Ag   94  -0.817  -0.817  -0.817
  0095Clust   Ag   95  -0.613  -0.613  -0.817
  0096Clust   Ag   96  

[gmx-users] How to choose appropriate size for a sliding average for smoothing distances between molecule types

[Anna Duncan]

I have performed a simulation of a protein in a lipid bilayer and I
want to look at the lengths of time that a particular lipid type, lipid
type A, say, remains within a certain distance of the protein.

I have calculated the distances between lipid type A and the protein.
Obviously, the trajectories of each particle are not smooth, so neither
are the distances between atoms of lipid type A and the protein.
Because I want to look at a continuous amounts of time that lipid type 
A

molecules are proximal to the protein, it seems to make sense to smooth
the distances, using xmgrace, for instance.  Does this make sense to
you?  If so, how should I go about determining by how much to smooth 
the

distances, or indeed the atom trajectories?  Is it worth looking at the
velocity autocorrelations or is this a slightly different question?


Many thanks,

Anna

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[gmx-users] Generation of 1-4 nonbonded parameters for CHARMM ff

[이종화]

 Hello,I'm trying to use CGENFF to generate CHARMM topology and parameter for a small molecule, and then convert the topology with charmm2gromacs program. I have some questions on the process.
 1) How is the 1-4 parameters generated from the CGENFF file? I was not able to find the parameters corresponding to the 1-4 nonbonded parameters in the original CHARMM parameter file.I'm trying to modify some parts of the topology and parameter obtained from PARAMCHEM(adding new atomtypes, etc) and is curious if this may result in inconsistency of generated 1-4 parameters.2) As I understand from the CHARMM implementation paper of GROMACS, special features of CHARMM(multiple dihedrals, CMAP, etc) has been taken into the GROMACS package. I'm not sure at which step this is done. I guess maybe pdb2gmx does when it generates .top file, and this is taken into account when grompp processes .top file. Am I correct?Thanks all in advance. I'm really appreciating the various features possible with GROMACS.Jong Wha






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FW: [gmx-users] Gromacs + Mopac error

[raul arias]

I used Ubuntu 12.10 64bit and gcc version 4.6.3. 
When I try to use the precompiled version of libmopac.a give me this error:
/usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching for 
-lmopac
/usr/bin/ld: cannot find -lmopac
collect2: ld returned 1 exit status

when I used this configure:
./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS=-lmopac 
-lgfortran LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib CPPFLAGS=-DUSE_MOPAC 
-I/home/raul/fftw/include --with-fft=fftw3 --disable-float --with-qmmm-mopac
Installation is fine!!

In the calculation of qmmm, Gromacs try searching the libraries of qm from 
gaussian.
Whe I use AM1 method, give me this error:
Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913
Fatal error:
Call to '(null)/(null)  input.com  input.log' failed

But, when i use RHF method, gave me other error:
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G*

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[raulxbsrk001:00965] *** Process received signal ***
[raulxbsrk001:00965] Signal: Segmentation fault (11)
[raulxbsrk001:00965] Signal code: Address not mapped (1)
[raulxbsrk001:00965] Failing at address: (nil)
[raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) 
[0x7fbaa74c1cb0]
[raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) 
[0x7fbaa717c101]
[raulxbsrk001:00965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x1e) 
[0x7fbaa716256e]
[raulxbsrk001:00965] [ 3] 
/home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_gaussian+0x48f) 
[0x7fbaa838cd1f]
[raulxbsrk001:00965] [ 4] 
/home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_QMMMrec+0x135c) 
[0x7fbaa837cbec]
[raulxbsrk001:00965] [ 5] /home/raul/gromacs_mopac/bin/mdrun_d(mdrunner+0x1269) 
[0x41e6d9]
[raulxbsrk001:00965] [ 6] /home/raul/gromacs_mopac/bin/mdrun_d(main+0x142e) 
[0x406bee]
[raulxbsrk001:00965] [ 7] 
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbaa711476d]
[raulxbsrk001:00965] [ 8] /home/raul/gromacs_mopac/bin/mdrun_d() [0x406e8d]
[raulxbsrk001:00965] *** End of error message ***
Violación de segmento (`core' generado)

Thank you very much for your patience and intentions to help me

 From: j...@um.es
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] Gromacs + Mopac error
 Date: Thu, 10 Jan 2013 14:32:43 +
 
 Hi Raul
 
 I'd need to see the exact errors you get to be able to help you, and 
 other info such as which OS and compilers are you using. From your 
 previous post, it seemed that the mopac interface was not being compiled 
 with gromacs, but gaussian or orca ones were, according to the errors 
 you showed (note they mention gaussian.c and qm_orca.c)
 
 The steps in the gromacs web should work (note you have to change some 
 files), and if not you can also try the precompiled library (libmopac.a, 
 in the same page). If you want to compile it by yourself, you can get 
 MOPAC code from http://openmopac.net/Downloads/Downloads.html (select 
 MOPAC7). Still, there might be some issues when compiling libmopac or in 
 runtime, but in such a case, we'd need to see what actual 
 errors/warnings are you observing (in your last mail it looked like the 
 installation went perfectly).
 
 Additionally, in case it could be of some help, I reported a 
 installation of gromacs-mopac in this mailing list some time ago
 http://lists.gromacs.org/pipermail/gmx-users/2011-November/066133.html
 
 Try all that and report back if you encounter any problem
 
 Javier
 
 
 El 10/01/13 14:59, raul arias escribió:
  Hi Javier,
  Thanks for your answer.
  I apologize for the delay in responding, but it's better with orca compiled 
  version.
  Now I'm trying to compile with mopac again, but I think that my mistake is 
  how to compile mopac.
  I'm following the steps of:
  http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM
 
 
  But in the version mopac7-1.11 has a subdirectory called fortran where 
  the codes are.
  Also, here mopac.f file does not exist, but if the file mopac7app.f (I have 
  to delete this? Like as deriv.f and moldat.f files)
  Can you help me at that point?
 
 
  From: j...@um.es
  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] Gromacs + Mopac error
  Date: Tue, 8 Jan 2013 08:59:31 +
 
  Hi
 
  The problem is that in your first try the gaussian interface is being
  used, while in the second the orca interface is used.
 
  The first try should have used the mopac interface but it apparently
  ignored it, the reason why must be written in the configure output.
  Could you show the last lines of such output? or clean the installation
  directory and try again configure (using the options you mentioned
  first, or you can add both --withoiut-qmmm-gaussian --with-qmmm-mopac) +
  make + make install and provide the last lines of each output?
 
  Javier
 
  El 

Re: FW: [gmx-users] Gromacs + Mopac error

[Javier Cerezo]

There is one point you have to note: although the qmmm interface  of 
gromacs can be applied with different codes (gaussian, orca, mopac..), 
only ONE must be selected at compilation. That is, if you have a mdrun 
binary compiled with gaussian-qmmm, all qmmm computations will use the 
gaussian interface.


So, according to the error in the output, specifically at:

Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913

It is observed that your installation was done with with the gaussian 
interface (that's what qm_gaussian.c is) not with mopac. Since in order 
to use the gaussian interface you need to meet some requirements (i.e. 
to have a specifically modified gaussian binary) you obtain an error as 
you are experiencing.


So, even if you think the installation is correct, something is not 
going well. I remember that special caution had to be taken if you first 
configure --with-qmmm-gaussian (this is the default) and then you try to 
compile again with other qmmm interface. So, make clean is required 
prior to a new installation. To sum up again: you have to realize that 
something strange is going on, since even if you include 
--with-qmmm-mopac, the gaussian interface is being used, and the first 
step to solve your problem is to be sure that you make your installation 
with mopac (not gaussian). Try make clean the directory, adding 
--without-qmmm-gaussian... Also inspect the output of configure to see 
why gaussian interface is used.


Javier

El 10/01/13 16:45, raul arias escribió:

I used Ubuntu 12.10 64bit and gcc version 4.6.3.
When I try to use the precompiled version of libmopac.a give me this error:
/usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching for 
-lmopac
/usr/bin/ld: cannot find -lmopac
collect2: ld returned 1 exit status

when I used this configure:
./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS=-lmopac 
-lgfortran LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib CPPFLAGS=-DUSE_MOPAC 
-I/home/raul/fftw/include --with-fft=fftw3 --disable-float --with-qmmm-mopac
Installation is fine!!

In the calculation of qmmm, Gromacs try searching the libraries of qm from 
gaussian.
Whe I use AM1 method, give me this error:
Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913
Fatal error:
Call to '(null)/(null)  input.com  input.log' failed

But, when i use RHF method, gave me other error:
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G*

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[raulxbsrk001:00965] *** Process received signal ***
[raulxbsrk001:00965] Signal: Segmentation fault (11)
[raulxbsrk001:00965] Signal code: Address not mapped (1)
[raulxbsrk001:00965] Failing at address: (nil)
[raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) 
[0x7fbaa74c1cb0]
[raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) 
[0x7fbaa717c101]
[raulxbsrk001:00965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x1e) 
[0x7fbaa716256e]
[raulxbsrk001:00965] [ 3] 
/home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_gaussian+0x48f) 
[0x7fbaa838cd1f]
[raulxbsrk001:00965] [ 4] 
/home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_QMMMrec+0x135c) 
[0x7fbaa837cbec]
[raulxbsrk001:00965] [ 5] /home/raul/gromacs_mopac/bin/mdrun_d(mdrunner+0x1269) 
[0x41e6d9]
[raulxbsrk001:00965] [ 6] /home/raul/gromacs_mopac/bin/mdrun_d(main+0x142e) 
[0x406bee]
[raulxbsrk001:00965] [ 7] 
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fbaa711476d]
[raulxbsrk001:00965] [ 8] /home/raul/gromacs_mopac/bin/mdrun_d() [0x406e8d]
[raulxbsrk001:00965] *** End of error message ***
Violación de segmento (`core' generado)

Thank you very much for your patience and intentions to help me


From: j...@um.es
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Gromacs + Mopac error
Date: Thu, 10 Jan 2013 14:32:43 +

Hi Raul

I'd need to see the exact errors you get to be able to help you, and
other info such as which OS and compilers are you using. From your
previous post, it seemed that the mopac interface was not being compiled
with gromacs, but gaussian or orca ones were, according to the errors
you showed (note they mention gaussian.c and qm_orca.c)

The steps in the gromacs web should work (note you have to change some
files), and if not you can also try the precompiled library (libmopac.a,
in the same page). If you want to compile it by yourself, you can get
MOPAC code from http://openmopac.net/Downloads/Downloads.html (select
MOPAC7). Still, there might be some issues when compiling libmopac or in
runtime, but in such a case, we'd need to see what actual
errors/warnings are you observing (in your last mail it looked like the
installation went perfectly).

Additionally, in case it could be of some help, I reported a
installation of gromacs-mopac in this mailing list some time ago

[gmx-users] Exclusions and pairs

[Ignacio Fernández Galván]

Dear Gromacs users:

Am I right assuming that [exclusions] do not affect the interactions defined by 
[pairs]?

This seems to be implied from the note in section 5.3.4 in the manual: Note 
that one should add exclusions for all atom pairs participating in pair 
interactions type 3, otherwise such pairs will also end up in the normal 
neighbor lists.

I think, however, that it can be confusing given the overall concept: 
[exclusions] removes non-bonded interactions, and [pairs] defines non-bonded 
interactions. One could think that pairs would be excluded too. May I suggest a 
more explicit statement to be added to the 5.4 sections (that [exclusions] do 
not affect [pairs]?

Ignacio
--
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

Re: [gmx-users] g_select error

[Teemu Murtola]

Hi,


On Thu, Jan 10, 2013 at 11:08 AM, Albert mailmd2...@gmail.com wrote:

  I am trying to use g_select to make an index file with command:

 g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx

 but it failed with messages:

 Assertion failed for g in file /home/albert/Desktop/gromacs-**
 4.6-beta3/src/gmxlib/sel
 dump core ? (y/n)


Could you please tell what you tried to select to cause this (the exact
selection string)? Without it, it is very difficult to investigate the
issue.

- Teemu
-- 
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

RE: [gmx-users] Gromacs + Mopac error

[raul arias]

Now I try with the options: --with-qmmm-mopac and --without-qmmm-gaussian at 
the same time.
same errors in config.log are:

configure:10166: mpicc -E -DUSE_MOPAC -I/home/raul/fftw/include conftest.cpp
conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:10166: $? = 1


configure:13309: mpicc -o conftest  -O3 -fomit-frame-pointer -finline-functions 
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast 
-DUSE_MOPAC -I/home/raul/fftw/include -L/home/raul/lib -L/home/raul/fftw/lib  
conftest.c -lmopac -lgfortran 5
/tmp/ccy92Ryd.o: In function `main':
conftest.c:(.text.startup+0x7): undefined reference to `shl_load'
collect2: ld returned 1 exit status
configure:13309: $? = 1


configure:24481: mpicc -c  -O3 -fomit-frame-pointer -finline-functions -Wall 
-Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast 
-DUSE_MOPAC -I/home/raul/fftw/include conftest.c 5
conftest.c:70:20: fatal error: direct.h: No such file or directory
compilation terminated.
configure:24481: $? = 1
I don't understand why gromacs did not take the mopac's library, because now 
tries to find qm from orca.
I guess I'll have to settle with orca. 
Thanks you for the help.


 From: j...@um.es
 To: gmx-users@gromacs.org
 Subject: Re: FW: [gmx-users] Gromacs + Mopac error
 Date: Thu, 10 Jan 2013 16:12:38 +
 
 There is one point you have to note: although the qmmm interface  of 
 gromacs can be applied with different codes (gaussian, orca, mopac..), 
 only ONE must be selected at compilation. That is, if you have a mdrun 
 binary compiled with gaussian-qmmm, all qmmm computations will use the 
 gaussian interface.
 
 So, according to the error in the output, specifically at:
 
 Program mdrun_d, VERSION 4.5.5
 Source code file: qm_gaussian.c, line: 913
 
 It is observed that your installation was done with with the gaussian 
 interface (that's what qm_gaussian.c is) not with mopac. Since in order 
 to use the gaussian interface you need to meet some requirements (i.e. 
 to have a specifically modified gaussian binary) you obtain an error as 
 you are experiencing.
 
 So, even if you think the installation is correct, something is not 
 going well. I remember that special caution had to be taken if you first 
 configure --with-qmmm-gaussian (this is the default) and then you try to 
 compile again with other qmmm interface. So, make clean is required 
 prior to a new installation. To sum up again: you have to realize that 
 something strange is going on, since even if you include 
 --with-qmmm-mopac, the gaussian interface is being used, and the first 
 step to solve your problem is to be sure that you make your installation 
 with mopac (not gaussian). Try make clean the directory, adding 
 --without-qmmm-gaussian... Also inspect the output of configure to see 
 why gaussian interface is used.
 
 Javier
 
 El 10/01/13 16:45, raul arias escribió:
  I used Ubuntu 12.10 64bit and gcc version 4.6.3.
  When I try to use the precompiled version of libmopac.a give me this error:
  /usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching 
  for -lmopac
  /usr/bin/ld: cannot find -lmopac
  collect2: ld returned 1 exit status
 
  when I used this configure:
  ./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS=-lmopac 
  -lgfortran LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib 
  CPPFLAGS=-DUSE_MOPAC -I/home/raul/fftw/include --with-fft=fftw3 
  --disable-float --with-qmmm-mopac
  Installation is fine!!
 
  In the calculation of qmmm, Gromacs try searching the libraries of qm from 
  gaussian.
  Whe I use AM1 method, give me this error:
  Program mdrun_d, VERSION 4.5.5
  Source code file: qm_gaussian.c, line: 913
  Fatal error:
  Call to '(null)/(null)  input.com  input.log' failed
 
  But, when i use RHF method, gave me other error:
  QM/MM calculation requested.
  there we go!
  Layer 0
  nr of QM atoms 22
  QMlevel: RHF/3-21G*
 
  number of CPUs for gaussian = 1
  memory for gaussian = 5000
  accuracy in l510 = 8
  NOT using cp-mcscf in l1003
  Level of SA at start = 0
  [raulxbsrk001:00965] *** Process received signal ***
  [raulxbsrk001:00965] Signal: Segmentation fault (11)
  [raulxbsrk001:00965] Signal code: Address not mapped (1)
  [raulxbsrk001:00965] Failing at address: (nil)
  [raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) 
  [0x7fbaa74c1cb0]
  [raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) 
  [0x7fbaa717c101]
  [raulxbsrk001:00965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(fputs+0x1e) 
  [0x7fbaa716256e]
  [raulxbsrk001:00965] [ 3] 
  /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_gaussian+0x48f) 
  [0x7fbaa838cd1f]
  [raulxbsrk001:00965] [ 4] 
  /home/raul/gromacs_mopac/lib/libmd_mpi_d.so.6(init_QMMMrec+0x135c) 
  [0x7fbaa837cbec]
  [raulxbsrk001:00965] [ 5] 
  /home/raul/gromacs_mopac/bin/mdrun_d(mdrunner+0x1269) [0x41e6d9]
  [raulxbsrk001:00965] [ 6] 

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

On Thu, Jan 10, 2013 at 7:25 AM, James Starlight jmsstarli...@gmail.comwrote:

 Szilárd ,

  thanks again for explanation!

 Today I've performed some tests on my calmodulin in water system with
 different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
 respectually)

 Below you can see that the highest performance was in case of 0.8 cut-offs

 all cut-offs 1.0
  Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305

 NOTE: The GPU has 20% more load than the CPU. This imbalance causes
   performance loss, consider using a shorter cut-off and a finer PME
 grid.


Core t (s)   Wall t (s)(%)
Time: 1313.420  464.035  283.0
  (ns/day)(hour/ns)
 Performance:9.3102.578
 Finished mdrun on node 0 Thu Jan 10 09:39:23 2013


 all cut-offs 0.9
 Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059

Core t (s)   Wall t (s)(%)
Time: 2414.930  856.179  282.1
  (ns/day)(hour/ns)
 Performance:   10.0922.378
 Finished mdrun on node 0 Thu Jan 10 10:09:52 2013

 all cut-offs 0.8
  Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859

Core t (s)   Wall t (s)(%)
Time: 1166.390  413.598  282.0
  (ns/day)(hour/ns)
 Performance:   10.4452.298
 Finished mdrun on node 0 Thu Jan 10 09:50:33 2013

 Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only
 67%. Is there any other ways to increase performance by means of
 neighboor search parameters ( e.g nstlist etc) ?


You can tweak nstlist and it often helps to increase it with GPUs,
especially in parallel. However, as increasing nstlist requires larger
rlist and more non-bonded calculations, this will not help you. You can try
to decrease it to 10-15 which will increase the NS cost but decrease the
GPU time, but it won't change the performance dramatically.

What's strange is that your Core time/Wall time = (%) is quite low. If
you're running on four threads on an otherwise empty machine, you should
get close to 400 if the threads are not idling, e.g waiting for the GPU.
For instance in the rc=0.8 case you can see that the GPU/CPU balance is
1.0 meaning that the GPU has less work than the CPU, case in which there
should be no idling and you should be getting (%) = 400.

Long story short: are you sure you're not running anything else on the
computer while simulating? What do you get if you run on CPU only?

Might such reduced cut-off be used with the force fields ( e,g charmm)
 where initially usage of longest cut-offs have given better results
 (e,g in charmm27 and gromos56 I always use 1.2 and 1.4 nm for rvdw,
 respectually) ?


No, at least not without *carefully* checking whether a shorter LJ cut-off
makes sense and that it does not break the physics of your simulation.

Although we advise you to consider decreasing your cut-off - mostly because
these days a large number of simulations are carried out with overly long
cut-off chosen by the rule of thumb or folclore -, you should always either
make sure that this makes sense before doing it or not do it at all.

Cheers,
--
Szilárd




 James

 2013/1/10 Szilárd Páll szilard.p...@cbr.su.se:
  Hi James,
 
  The build looks mostly fine except that you are using fftw3 compiled with
  AVX which is slower than with only SSE (even on AVX-capable CPUs) - you
  should have been warned about this at configure-time.
 
  Now, performance-wise everything looks fine except that with a 1.2 nm
  cut-off your GPU is not able to keep up with the CPU and finish the
  non-bonded work before the CPU is done with Bonded + PME. That's why you
  see the Wait GPU taking 20% of the total time and that's also why you
 see
  some cores idling (because for 20% of the run-time thread 0 on core 0
  is blocked waiting for the GPU while the rest idle).
 
  As the suggestion at the end of the log file point out, you can consider
  using a shorter cut-off which will push more work back to the PME on the
  CPU, but whether you can do this it depends on your very problem.
 
  There is one more alternative of running two MPI processes on the GPU
  (mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will
  execute part of the nonbonded on the CPU, but this might not help.
 
  Cheers,
 
  --
  Szilárd
 
 
  On Wed, Jan 9, 2013 at 8:27 PM, James Starlight jmsstarli...@gmail.com
 wrote:
 
  Dear Szilárd, thanks for help again!
 
  2013/1/9 Szilárd Páll szilard.p...@cbr.su.se:
 
  
   There could be, but I/we can't well without more information on what
 and
   how you compiled and ran. The minimum we need is a log file.
  
  I've compilated gromacs 4.6-3 beta via simple
 
 
  cmake CMakeLists.txt -DGMX_GPU=ON
  -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
  make
  sudo make install
 
  I have not added any special params to the grompp or mdrun.
 
  After that I've run tested simulation of the 

Re: [gmx-users] Gromacs 4.6 turn off ecc

[Szilárd Páll]

Hi,

Note that the CUDA NxN non-bonded kernels are programmer and
performance-tuned in such a way that they have very high compute/memory
access ratio and therefore are not sensitive to GPU memory performance.
Hence with the native GPU acceleration you won't see any improvement from
turning off ECC.

Cheers,

--
Szilárd


On Thu, Jan 10, 2013 at 12:30 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 1/10/13 5:43 AM, sebastian wrote:

 Dear Gromacs user,

 is there a way to manually  turn off ECC (gromacs version 4.6)?


 That's outside of Gromacs.  Google has lots to say...

 http://nvidia.helpmax.net/en/**workstation/ecc-state-control/**
 how-do-i/turn-my-gpu-ecc-on-**or-off/http://nvidia.helpmax.net/en/workstation/ecc-state-control/how-do-i/turn-my-gpu-ecc-on-or-off/

 -Justin

 --
 ==**==

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

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Re: [gmx-users] Gromacs + Mopac error

[Javier Cerezo]

Did you clean your directoy (make clean)? It tries with orca because 
that's the default behaviour when gaussian is disabled. Somehow, it's 
completely ignoring the --with-qmmm-mopac instruction. And, which 
gromacs version are you trying to build, did you try with a previous 
version?


Also, note that parallelization cannot be used in the gromacs part when 
a qmmm interface is requested. So, it can save some problems if you 
disable threads and mpi to build the binary for qmmm.


Javier

El 10/01/13 19:07, raul arias escribió:

Now I try with the options: --with-qmmm-mopac and --without-qmmm-gaussian at 
the same time.
same errors in config.log are:

configure:10166: mpicc -E -DUSE_MOPAC -I/home/raul/fftw/include conftest.cpp
conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:10166: $? = 1


configure:13309: mpicc -o conftest  -O3 -fomit-frame-pointer -finline-functions -Wall 
-Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -DUSE_MOPAC 
-I/home/raul/fftw/include -L/home/raul/lib -L/home/raul/fftw/lib  conftest.c -lmopac 
-lgfortran 5
/tmp/ccy92Ryd.o: In function `main':
conftest.c:(.text.startup+0x7): undefined reference to `shl_load'
collect2: ld returned 1 exit status
configure:13309: $? = 1


configure:24481: mpicc -c  -O3 -fomit-frame-pointer -finline-functions -Wall 
-Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -DUSE_MOPAC 
-I/home/raul/fftw/include conftest.c 5
conftest.c:70:20: fatal error: direct.h: No such file or directory
compilation terminated.
configure:24481: $? = 1
I don't understand why gromacs did not take the mopac's library, because now 
tries to find qm from orca.
I guess I'll have to settle with orca.
Thanks you for the help.



From: j...@um.es
To: gmx-users@gromacs.org
Subject: Re: FW: [gmx-users] Gromacs + Mopac error
Date: Thu, 10 Jan 2013 16:12:38 +

There is one point you have to note: although the qmmm interface  of
gromacs can be applied with different codes (gaussian, orca, mopac..),
only ONE must be selected at compilation. That is, if you have a mdrun
binary compiled with gaussian-qmmm, all qmmm computations will use the
gaussian interface.

So, according to the error in the output, specifically at:

Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913

It is observed that your installation was done with with the gaussian
interface (that's what qm_gaussian.c is) not with mopac. Since in order
to use the gaussian interface you need to meet some requirements (i.e.
to have a specifically modified gaussian binary) you obtain an error as
you are experiencing.

So, even if you think the installation is correct, something is not
going well. I remember that special caution had to be taken if you first
configure --with-qmmm-gaussian (this is the default) and then you try to
compile again with other qmmm interface. So, make clean is required
prior to a new installation. To sum up again: you have to realize that
something strange is going on, since even if you include
--with-qmmm-mopac, the gaussian interface is being used, and the first
step to solve your problem is to be sure that you make your installation
with mopac (not gaussian). Try make clean the directory, adding
--without-qmmm-gaussian... Also inspect the output of configure to see
why gaussian interface is used.

Javier

El 10/01/13 16:45, raul arias escribió:

I used Ubuntu 12.10 64bit and gcc version 4.6.3.
When I try to use the precompiled version of libmopac.a give me this error:
/usr/bin/ld: skipping incompatible /home/raul/lib/libmopac.a when searching for 
-lmopac
/usr/bin/ld: cannot find -lmopac
collect2: ld returned 1 exit status

when I used this configure:
./configure --enable-mpi --prefix=/home/raul/gromacs_mopac LIBS=-lmopac 
-lgfortran LDFLAGS=-L/home/raul/lib -L/home/raul/fftw/lib CPPFLAGS=-DUSE_MOPAC 
-I/home/raul/fftw/include --with-fft=fftw3 --disable-float --with-qmmm-mopac
Installation is fine!!

In the calculation of qmmm, Gromacs try searching the libraries of qm from 
gaussian.
Whe I use AM1 method, give me this error:
Program mdrun_d, VERSION 4.5.5
Source code file: qm_gaussian.c, line: 913
Fatal error:
Call to '(null)/(null)  input.com  input.log' failed

But, when i use RHF method, gave me other error:
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: RHF/3-21G*

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[raulxbsrk001:00965] *** Process received signal ***
[raulxbsrk001:00965] Signal: Segmentation fault (11)
[raulxbsrk001:00965] Signal code: Address not mapped (1)
[raulxbsrk001:00965] Failing at address: (nil)
[raulxbsrk001:00965] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) 
[0x7fbaa74c1cb0]
[raulxbsrk001:00965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x89101) 
[0x7fbaa717c101]
[raulxbsrk001:00965] [ 2] 

[gmx-users] Calculation of parameters

[Bharath K. Srikanth]

Hi

Is it possible to use the GROMACS methods g_msd or g_velacc to calculate
parameters (i.e the diffusion coefficient) when the parameter value varies
with position (eg. diffusion of a nanoparticle through a lipid bilayer)?
If so, how?

If not, are there any other GROMACS methods that can be used to obtain
this position-dependent diffusion coefficient from a trajectory file?

Thanks a lot!

Sincerely
Bharath


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Re: [gmx-users] Exclusions and pairs

[Justin Lemkul]

On 1/10/13 11:14 AM, Ignacio Fernández Galván wrote:

Dear Gromacs users:

Am I right assuming that [exclusions] do not affect the interactions defined by 
[pairs]?

This seems to be implied from the note in section 5.3.4 in the manual: Note that 
one should add exclusions for all atom pairs participating in pair interactions type 3, 
otherwise such pairs will also end up in the normal neighbor lists.

I think, however, that it can be confusing given the overall concept: 
[exclusions] removes non-bonded interactions, and [pairs] defines non-bonded 
interactions. One could think that pairs would be excluded too. May I suggest a 
more explicit statement to be added to the 5.4 sections (that [exclusions] do 
not affect [pairs]?



Pairs are bonded interactions.

http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html

The type 3 pair you're referring to has a very specific use in free energy 
calculations, and that section of the manual has actually been re-written for 
version 4.6 and the usage changed to require a [pairs_nb] directive to indicate 
special nonbonded interactions in that case.  I think the newer explanation is 
slightly clearer than before.


-Justin

--


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Research Scientist
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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Re: [gmx-users] How to choose appropriate size for a sliding average for smoothing distances between molecule types

[Justin Lemkul]

On 1/10/13 10:07 AM, Anna Duncan wrote:


I have performed a simulation of a protein in a lipid bilayer and I
want to look at the lengths of time that a particular lipid type, lipid
type A, say, remains within a certain distance of the protein.

I have calculated the distances between lipid type A and the protein.
Obviously, the trajectories of each particle are not smooth, so neither
are the distances between atoms of lipid type A and the protein.
Because I want to look at a continuous amounts of time that lipid type A
molecules are proximal to the protein, it seems to make sense to smooth
the distances, using xmgrace, for instance.  Does this make sense to
you?  If so, how should I go about determining by how much to smooth the
distances, or indeed the atom trajectories?  Is it worth looking at the
velocity autocorrelations or is this a slightly different question?



I don't understand why you would smooth the data.  From the description, it 
seems like you are trying to determine the length of time that the lipid is 
within a certain distance of the protein as a measure of its interaction.  The 
raw data should be sufficient to accomplish that.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] Calculation of parameters

[Justin Lemkul]

On 1/10/13 1:59 PM, Bharath K. Srikanth wrote:

Hi

Is it possible to use the GROMACS methods g_msd or g_velacc to calculate
parameters (i.e the diffusion coefficient) when the parameter value varies
with position (eg. diffusion of a nanoparticle through a lipid bilayer)?
If so, how?

If not, are there any other GROMACS methods that can be used to obtain
this position-dependent diffusion coefficient from a trajectory file?



Presumably you should be able to analyze the diffusion during different time 
frames within the trajectory using -b and -e with any command.  That would allow 
you to measure diffusion constants in different environments, assuming you have 
enough data in each environment to make reasonable observations.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] gromacs on GPU

[James Starlight]

Szilárd,

There are no any others cpu-usage tasks. Below you can see log from the TOP.

26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun
 1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77 mate-system-mon
 2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
   10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
   12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
   13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
   15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
   16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
   17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
   19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
   20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
   21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
   22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
   23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs


Usually I run my simulations by means of simple mdrun -v -deffnm md.
Should I specify number of cores manually by means of -nt (or -ntmpi)
flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
support. Does it reasonable in the simulation on cpu+gpu ? What
another possible options of md_run should I consider ? Finally is it
possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
drivers ?


Thanks for help

James


2013/1/10 Szilárd Páll szilard.p...@cbr.su.se:
 On Thu, Jan 10, 2013 at 7:25 AM, James Starlight 
 jmsstarli...@gmail.comwrote:

 Szilárd ,

  thanks again for explanation!

 Today I've performed some tests on my calmodulin in water system with
 different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
 respectually)

 Below you can see that the highest performance was in case of 0.8 cut-offs

 all cut-offs 1.0
  Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305

 NOTE: The GPU has 20% more load than the CPU. This imbalance causes
   performance loss, consider using a shorter cut-off and a finer PME
 grid.


Core t (s)   Wall t (s)(%)
Time: 1313.420  464.035  283.0
  (ns/day)(hour/ns)
 Performance:9.3102.578
 Finished mdrun on node 0 Thu Jan 10 09:39:23 2013


 all cut-offs 0.9
 Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059

Core t (s)   Wall t (s)(%)
Time: 2414.930  856.179  282.1
  (ns/day)(hour/ns)
 Performance:   10.0922.378
 Finished mdrun on node 0 Thu Jan 10 10:09:52 2013

 all cut-offs 0.8
  Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859

Core t (s)   Wall t (s)(%)
Time: 1166.390  413.598  282.0
  (ns/day)(hour/ns)
 Performance:   10.4452.298
 Finished mdrun on node 0 Thu Jan 10 09:50:33 2013

 Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only
 67%. Is there any other ways to increase performance by means of
 neighboor search parameters ( e.g nstlist etc) ?


 You can tweak nstlist and it often helps to increase it with GPUs,
 especially in parallel. However, as increasing nstlist requires larger
 rlist and more non-bonded calculations, this will not help you. You can try
 to decrease it to 10-15 which will increase the NS cost but decrease the
 GPU time, but it won't change the performance dramatically.

 What's strange is that your Core time/Wall time = (%) is quite low. If
 you're running on four threads on an otherwise empty machine, you should
 get close to 400 if the threads are not idling, e.g waiting for the GPU.
 For instance in the rc=0.8 case you can see that the GPU/CPU balance is
 1.0 meaning that the GPU has less work than the CPU, case in which there
 should be no idling and you should be getting (%) = 400.

 Long story short: are you sure you're not running anything else on the
 computer while simulating? What do you get if you run on CPU only?

 Might such reduced cut-off be used with the force 

Re: [gmx-users] g_select error

[Roland Schulz]

Hi,

thanks for the bug report. Please let us know whether:
https://gerrit.gromacs.org/#/c/2014/

fixes it.

Roland


On Thu, Jan 10, 2013 at 4:08 AM, Albert mailmd2...@gmail.com wrote:

 hello:

   I am trying to use g_select to make an index file with command:


 g_select_mpi -f md.xtc -s npt3.pdb -on density.ndx

 but it failed with messages:

 WARNING: Masses and atomic (Van der Waals) radii will be guessed
   based on residue and atom names, since they could not be
   definitively assigned from the information in your input
   files. These guessed numbers might deviate from the mass
   and radius of the atom type. Please check the output
   files if necessary.

 Assertion failed for g in file
 /home/albert/Desktop/gromacs-4.6-beta3/src/gmxlib/sel
 dump core ? (y/n)


 thank you very much
 Albert
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Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

Hi,

On Thu, Jan 10, 2013 at 8:30 PM, James Starlight jmsstarli...@gmail.comwrote:

 Szilárd,

 There are no any others cpu-usage tasks. Below you can see log from the
 TOP.

 26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun


This still shows that the average CPU utilization is only 285.6 iso 400 and
that matches with what mdrun's log shows. Try to run with a very short
cut-off, one which leads to =1 GPU/CPU balance (i.e no waiting) and if you
still don't get 400, something weird is going on.


  1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
 29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77
 mate-system-mon
  2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
 29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
 29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
 29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
 29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
 1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
 2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
 3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
 6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
 7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
 8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs


 Usually I run my simulations by means of simple mdrun -v -deffnm md.
 Should I specify number of cores manually by means of -nt (or -ntmpi)


If you just want to run on the full machine, simply running like that
should in most cases still be the optimal run configuration or very close
to the optimal, i.e. in your case:
mdrun
=
mdrun -ntmpi 1 -ntomp 4 -gpu_id 0 -pinht


 flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
 support. Does it reasonable in the simulation on cpu+gpu ? What


Correctly using HT is also fully automatic and optimal as long as you are
using the full machine.


 another possible options of md_run should I consider ? Finally is it
 possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
 drivers ?


No, you are using the latest version of compilers which is good. Other than
my earlier suggestions, there isn't much you can do to eliminate the idling
on the CPU (I assume that's what bugs you) - except getting a faster GPU.
Btw, have you tried the hybrid GPU-CPU mode (although I expect it to not be
faster)?

Cheers,
--
Szilárd





 Thanks for help

 James


 2013/1/10 Szilárd Páll szilard.p...@cbr.su.se:
  On Thu, Jan 10, 2013 at 7:25 AM, James Starlight jmsstarli...@gmail.com
 wrote:
 
  Szilárd ,
 
   thanks again for explanation!
 
  Today I've performed some tests on my calmodulin in water system with
  different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
  respectually)
 
  Below you can see that the highest performance was in case of 0.8
 cut-offs
 
  all cut-offs 1.0
   Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305
 
  NOTE: The GPU has 20% more load than the CPU. This imbalance causes
performance loss, consider using a shorter cut-off and a finer PME
  grid.
 
 
 Core t (s)   Wall t (s)(%)
 Time: 1313.420  464.035  283.0
   (ns/day)(hour/ns)
  Performance:9.3102.578
  Finished mdrun on node 0 Thu Jan 10 09:39:23 2013
 
 
  all cut-offs 0.9
  Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059
 
 Core t (s)   Wall t (s)(%)
 Time: 2414.930  856.179  282.1
   (ns/day)(hour/ns)
  Performance:   10.0922.378
  Finished mdrun on node 0 Thu Jan 10 10:09:52 2013
 
  all cut-offs 0.8
   Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859
 
 Core t (s)   Wall t (s)(%)
 Time: 1166.390  413.598  282.0
   (ns/day)(hour/ns)
  Performance:   10.4452.298
  Finished mdrun on node 0 Thu Jan 10 09:50:33 2013
 
  Also I've noticed that 2-4 CPU cores usage in 

Re: [gmx-users] The number of lipids

[Justin Lemkul]

On 1/10/13 8:03 PM, Kieu Thu Nguyen wrote:

Dear All,

I see in MD simulations, the number of lipids is 128 or multiples of 128.
Can someone tell me why ?


Probably convenience (easy to create 8 x 8 grid for each layer) and adequate 
sampling.



Whether can i choose another number of lipids ?



Sure, if you can produce a suitable configuration and gather sufficient data. 
Carving out a subset of lipids from an existing bilayer is hard because you 
probably won't get a regular shape, but you can create your own bilayers if you 
like.  If you want more lipids, you can multiply any existing bilayer simply by 
using genconf -nbox.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Re: [gmx-users] The number of lipids

[Peter Lai]

Kieu Thu Nguyen kieuthu2...@gmail.com wrote:

Dear All,

I see in MD simulations, the number of lipids is 128 or multiples of
128.
Can someone tell me why ?
Whether can i choose another number of lipids ?

Thanks in advance !
KT
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probably because they are using original 128-lipid coordinates from someone 
like tieleman or klauda. You can use any arbitrary # of lipids appropriate to 
the size of your intended system (like scaling it so that an embedded protein 
is shielded by lipids from its periodic image)
-- 
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[gmx-users] question about dihedral constraints

[Tom]

Dear Gromacs Users,

I want to use dihedral constraint in gmx.

I directly type the following onto my  topol.top file :
--
[ dihedral_restraints ]
; ai   ajakal  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
   506505 502503 1  1  180 0 1  2
--

Do I also need to add these to *mdp file?
---
dihre = yes
dihre_fc  = 15000
-
Because I only need to contraint some of the dihedrals,
I will  not constraints all of them.
If I add the above on  *mdp file, will all the dihedrals be constrainted?

Another quesiton is what is the format of this dihedral constraints
on *rtp file? How about the angle constraints? That would save a lot
of work if pdb2gmx can automatically add these constraints to *top file.

Thanks a lot for the help!

Steven
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Re: [gmx-users] question about dihedral constraints

[Justin Lemkul]

On 1/10/13 9:28 PM, Tom wrote:

Dear Gromacs Users,

I want to use dihedral constraint in gmx.



First, you should understand that constraints and restraints refer to very 
different ideas:


http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints


I directly type the following onto my  topol.top file :
--
[ dihedral_restraints ]
; ai   ajakal  type  label  phi  dphi  kfac  power
; phi C'(n-1) - N - CA - C'
506505 502503 1  1  180 0 1  2
--

Do I also need to add these to *mdp file?
---
dihre = yes
dihre_fc  = 15000
-


Everything you need to know is either in the manual or on the website:

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


Because I only need to contraint some of the dihedrals,
I will  not constraints all of them.
If I add the above on  *mdp file, will all the dihedrals be constrainted?



A simple test should be very illuminating.  You will get a dihedral restraint 
energy written to the .log and .edr files, and either your dihedral will be 
restrained or not (easily measured by g_angle).



Another quesiton is what is the format of this dihedral constraints
on *rtp file? How about the angle constraints? That would save a lot
of work if pdb2gmx can automatically add these constraints to *top file.



That's what genrestr is for.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Generation of 1-4 nonbonded parameters for CHARMMff

[Jong Wha Lee]

- I apologize for resubmitting the question as my previous mail was not
properly sent.

 

Dear gromacs users,

 

I'm trying to build a new topology and a parameter file of a small organic
molecule. My strategy is to use CGENFF(and  http://paramchem.org/
paramchem.org) to generate CHARMM topology and parameter, and then convert
the topology with charmm2gromacs program. I have some questions on the
process.

 

1) How is the 1-4 parameters generated from the CGENFF file(or more
generally, from charmm ff?)? I was not able to find the parameters
corresponding to the 1-4 nonbonded parameters in original CHARMM parameter
files.

 I'd like to modify some parts of the topology and parameter obtained from
http://paramchem.org/ paramchem.org(adding new atomtypes, and change
charges etc) before using charmm2gromacs and is curious if this may result
in inconsistency of generated 1-4 parameters. Do I have to also change some
other parameters, such as CMAP, when I'm modifying the charges, bond force
constant, in the sake of correct 1-4 parameters?

 

2) As I understand from the CHARMM implementation paper of GROMACS, special
features of CHARMM(multiple dihedrals, CMAP, etc) has been taken into the
GROMACS package. I wonder at which step this is done. I guess maybe pdb2gmx
does when it generates .top file, and this is taken into account when grompp
processes .top file. I'm not sure if I'm correct.

 

 

Thanks all in advance. I'm really appreciating the various features possible
with GROMACS.

 

 

Jong Wha

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Re: [gmx-users] The number of lipids

[Kieu Thu Nguyen]

Thank Justin and Peter so much !
Can i make a new box (it's size is not a multiples of the size of the
previous box) from a smaller lipid bilayer box ?

I don't see genconf -nbox can do that.



On Fri, Jan 11, 2013 at 9:20 AM, Peter Lai p...@uab.edu wrote:

 Kieu Thu Nguyen kieuthu2...@gmail.com wrote:

 Dear All,
 
 I see in MD simulations, the number of lipids is 128 or multiples of
 128.
 Can someone tell me why ?
 Whether can i choose another number of lipids ?
 
 Thanks in advance !
 KT
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 probably because they are using original 128-lipid coordinates from
 someone like tieleman or klauda. You can use any arbitrary # of lipids
 appropriate to the size of your intended system (like scaling it so that an
 embedded protein is shielded by lipids from its periodic image)
 --
 Sent from my Android phone with K-9 Mail. Please excuse my brevity.
 --
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[gmx-users] mdp option for implicit solvent simulation

[Sanku M]

Hi,
  I am trying to do implicit solvent simulation for a protein in gas-phase. I 
have a few questions :
1) should I use sd integrator?

2) should I also use no periodic condition considering continuum dielectric ?

3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no 
cutoffs were used for implicit solvent simulations. 
 But, again in implicit solvent setup the rgblist should be equal to rlist.
Now, if I use rlist=0 ( as all interactions are considered), should I also make 
rgblist=0?
Does it mean the setup was following type: i.e.
 
  ; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 0
; ns algorithm (simple or grid)
ns-type                  = simple
; Periodic boundary conditions: xyz, no, xy
pbc                      = no
periodic_molecules       = no
; nblist cut-off
rlist                    = 0
; long-range cut-off for switched potentials
rlistlong                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = GBSA

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0.150
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
gb_dielectric_offset     = 0.009
sa_algorithm             = Ace-approximation
sa_surface_tension       = -1



Some idea about the implicit solvent setup will be appreciated.
Sanku
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Re: [gmx-users] gromacs on GPU

[James Starlight]

Szilárd,

the regime with 4 cores + cut-offs 0.8 has been best still.

  PID USER  PR  NI  VIRT  RES  SHR S  %CPU %MEMTIME+  COMMAND
 1652 own   20   0 28.4g 135m  33m R 288.8  0.8   4:30.33 mdrun

 Force evaluation time GPU/CPU: 5.257 ms/5.187 ms = 1.013
For optimal performance this ratio should be close to 1!


   Core t (s)   Wall t (s)(%)
   Time:  494.240  171.719  287.8
 (ns/day)(hour/ns)
Performance:   10.0642.385
Finished mdrun on node 0 Fri Jan 11 09:38:38 2013

I've tried to use compination of the different core numbers but
results was the same ( below example with the 2 cores +gpu)
  PID USER  PR  NI  VIRT  RES  SHR S  %CPU %MEMTIME+  COMMAND
 1578 own   20   0 28.3g 163m  33m R 170.7  1.0   1:50.68 mdrun


Also cut-offs lower that 0.8 produced the same results. When I've used
cut-off 0.1 the simulation have been crushed :) Finally increassing of
nstlist up to 50 also gave slightly better results ( cpu usage up to
295) but I'm not sure about influence os such large cutoofs on other
aspects of simulation.

On that tests I'm using cpu CPU Intel Core i5-3570 3.4 ГГц / 4core /
SVGA HD Graphics 2500 / 1+6Мб / as well as GPU GeForce GTX 670.

Also I want to point out that all simulation have been run from debian
GE GNOME desktope. Should I run simulation from console mode only to
kill all hidden cpu-dependent processes?

By the way I wounder to know is it possible to use 2 gpu at the same
time (in the SLI mode) ? How It might increase overasl performance ?
In future I'd like to built new work-station on 8 cores i7 CPU + 2
GPU. What the performance of such work-station will be? ( in
comparison to the typical cluster from several nodes of 8-12 cpu ) ?


Thanks for suggestions,
James

2013/1/11 Szilárd Páll szilard.p...@cbr.su.se:
 Hi,

 On Thu, Jan 10, 2013 at 8:30 PM, James Starlight 
 jmsstarli...@gmail.comwrote:

 Szilárd,

 There are no any others cpu-usage tasks. Below you can see log from the
 TOP.

 26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun


 This still shows that the average CPU utilization is only 285.6 iso 400 and
 that matches with what mdrun's log shows. Try to run with a very short
 cut-off, one which leads to =1 GPU/CPU balance (i.e no waiting) and if you
 still don't get 400, something weird is going on.


  1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
 29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77
 mate-system-mon
  2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
 29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
 29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
 29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
 29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
 1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
 2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
 3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
 6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
 7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
 8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs


 Usually I run my simulations by means of simple mdrun -v -deffnm md.
 Should I specify number of cores manually by means of -nt (or -ntmpi)


 If you just want to run on the full machine, simply running like that
 should in most cases still be the optimal run configuration or very close
 to the optimal, i.e. in your case:
 mdrun
 =
 mdrun -ntmpi 1 -ntomp 4 -gpu_id 0 -pinht


 flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
 support. Does it reasonable in the simulation on cpu+gpu ? What


 Correctly using HT is also fully automatic and optimal as long as you are
 using the full machine.


 another possible options of md_run should I consider ? Finally is it
 possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
 drivers ?


 No, you are using the latest version of compilers which is good. Other than