Re: [gmx-users] Interactions regarding

[Mark Abraham]

- Original Message -
From: rekkha nivethitha 
Date: Thursday, September 2, 2010 14:35
Subject: [gmx-users] Interactions regarding
To: gmx-users@gromacs.org

> > Hi..
> 
> I have simulated protein-protein complex using gromacs.
> Now, i have to see the interactions between the protein-protein complex.
> 
> How to see the interactions of active site residues.  Is there any molecular 
> viewer available for this study.

Viewing things is fairly easy. See 
http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/Visualization_Software

Quantifying anything is harder.

Mark

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[gmx-users] Interactions regarding

[rekkha nivethitha]

Hi..

I have simulated protein-protein complex using gromacs.
Now, i have to see the interactions between the protein-protein complex.

How to see the interactions of active site residues.  Is there any molecular
viewer available for this study.

Thank u..


-- 
S.T.B. Rekkha Nivethitha
MPhil, Department of Bioinformatics,
Structural Biology Lab,
Bharathiar University,
Coimbatore - 46.
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Re: [gmx-users] Newest version of Gromacs 4.5 installation

[Mark Abraham]

- Original Message -
From: Moeed 
Date: Thursday, September 2, 2010 6:44
Subject: [gmx-users] Newest version of Gromacs 4.5 installation
To: gmx-users@gromacs.org

> Hi,
> 
> We are installing the newest version of Gromacs - 4.5 on our cluster (running 
> CentOS) for parallel purposes. We are also using Openmpi version 1.4. However 
> upon installing Gromacs using the command:
> 
> 
> ./configure --enable-mpi
 > 
> 
> we ran into this problem below:
> 
> 
> * Seems you are compiling with MPI support. You can install the MPI-
>   enabled programs with suffixed names to have both MPI and non-MPI
>   versions. This is useful e.g. on supercomputers where you usually
>cannot run MPI-linked programs on the login node.
>   Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
>   You only need MPI for mdrun, so if you already have non-MPI stuff
>   installed you can issue make mdrun; make install-mdrun.
 > 
>   WARNING:
>   There are known problems with some MPI implementations:
>  OpenMPI version < 1.4.1
>  MVAPICH2 version <= 1.4.1
> 
> * On most platforms you can save 10X space with dynamic libraries, although
>the binaries might be less portable. Why not try --enable-shared ?
> 
> 
> Does this imply that we must update our current Openmpi version from 1.4 to 
> 1.41 in order for Gromacs to be installed?

No, it's only a warning. Feel free to ignore it, but if you get mystifying 
problems, upgrading MPI is your first port of call.

> Also, what are the pros and cons of using '--enable-shared'?

 Smaller installation footprint. Perhaps smaller code execution memory 
footprint. Potentially more work to do making sure the execution environment 
has access to the shared libraries as well as the executable. Mess if you 
mis-manage having multiple versions installed at the same time. More hassle in 
heterogenous computing environments.

Mark

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[gmx-users] Re: [gmx-developers] Free Energy Calculation

[Justin A. Lemkul]

As a preface, please note that the development list is not the appropriate forum 
for this question.  I am CC'ing this message to the gmx-users list.  Please post 
any future questions there.


Emanuel Birru wrote:

Hi,

 

I am doing a partition coefficient of solute between 1-Octanol and water 
using gromacs ffG53a6 force field. The first thing I have done is to 
predict the Gibbs free energy of salvation of pentane (my solute) in 
1-Octanol by thermodynamics integration method using 16 λ (lambda) 
values. The problem have stated on λ=0.6 and it is LINCS error which 
says as follows:


Fatal error:

Too many LINCS warnings (1001)

If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file or set the environment variable 
GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem


The atoms that make the problem are pentane atoms.



And what parameters are you using for both pentane and octanol?  Have you 
validated that they should otherwise run stably?  LINCS warnings usually come 
from insufficient minimization and/or equilibration, i.e.:


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

 

I have put the parameter file that I am using on this link 
http://hydra.pharm.monash.edu.au/md_project/production.txt


 

After I got the error I have tried to run it again by changing the time 
step and the soft core value i.e sc_alpha and run three jobs independently


1.   With 1fs time step and sc_alpha = 1.51

2.   With 2fs time step changing sc_alpha to 0.5 and

3.   With 1fs time step and 0.5 sc_alpha

The same problem happened for 2 and 3 but 1 works well, but the average 
dVpot/d λ is not what I expected, its >+7. I could not figure it out 
where exactly the problem is.




Regarding values for sc_alpha, there are some helpful tips and discussion in the 
free energy tutorial, specifically in the section:


http://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial#More_run_input_files

-Justin

 


Thanks in advance for your advise.

 


Cheers,

Emanuel

 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Re[17]: Flat energy profile in g_wham

[alexander yakovenko]

A solution of that thread: g_wham do not integrate properly is some part of 
profile covered with only a window. Particularly I was ale to integrate 
http://picasaweb.google.ca/117558205101329348732/G_wham#5511244561053627250 
with options -min 4.1 -max 5.8. With wider borders it's profile turns into flat 
line.   
Regards,  
Alex.  
  
  
  Let's keep this on the list for now please.  
  
Quoting alexander yakovenko :  
  
> Just to close this topic: pullf do corresponds pullx in *all* my MD  
> runs... so what is ideas about g_wham flat line (except low  
> population of samples)?  
> Regards,  
> Alex  
>  
>  
>  
> Alex, I would be happy to provide timely advice and direction in  
> exchange for middle-authorship. It would, however, need to go through  
> the proper channels in order to get my supervisor's approval. To  
> formally propose this, you could send an email to my and copy your  
> supervisor and my supervisor (po...@sickkids.ca). Perhaps you and I  
> should hash out what it might look like first though, before bothering  
> them. From my side, I would prefer if my contribution was limited to a  
> single aspect that could be well defined from the start -- I have had  
> too many arrangements spiral out of control into large bodies of work  
> when I don;t have time available for it.  
>  
> Regarding the "evidences", I am not sure what you mean. If you mean to  
> ask how did I know? well, I didn't really until you sent the data from  
> the water simulation. I took a look at the numbers and figured it out  
> -- but I wanted you to figure it out on your own to learn about the  
> process. It's just that I have developed a reductionist strategy to  
> debug problems that seems to work well and I've seen enough problems  
> to know that figuring out numbers and equations for single snapshots  
> is the best way to go. Simple systems too so that you can calulate it  
> by hand if you need to.  
>  
> I don't think that 10x more data is the solution that you need. You  
> should go back to the original data pullf and pullx files and see if  
> you can relate the pullf to the pullx there also.  
>  
> Finally, let's either hash out an authorship agreement or get this  
> back on the mailing list.  
>  
> Chris.  
>  
> Quoting alexander yakovenko :  
>  
>>  
>>  
>> Thank you Chris! I am really appreciating this.  
>>  
>> Definitely I would like to consult with you about this method.  
>> Actually I have no other choice as need to calculate differences in  
>> free energy of protein-DNA binding for wt and mutant and umbrella  
>> PMF looks like the only method I can carry this out (Jarzynski  
>> approach most probably is too demanding). There is a problem  
>> however: I can’t just consume your time. If you agree to consider  
>> (just consider!) an option to participate our publication where PMF  
>> is used to prove meaning of new distant mutation of MEF2B for  
>> cancer, then I wouldn’t fill myself like parasite. It would be  
>> rather cooperation which sounds much better, right :)? Don’t worry I  
>> am not going to bother you much: I have reasonable amount of  
>> computers, satisfactory skills with gromacs, empirical data about  
>> mutations so on... a bit experience with PMF is very welcome though.  
>>  
>> As for pullf I just forgotten to subtract initial displacement, now  
>> it fits perfect with pullx (Btw how can you judge about evidences  
>> from files I have sent? Just because it is so evident?). As for now  
>> I restarted mdruns with 0.2ns pull_nst?out, hope 10 times more  
>> points will contribute to g_wham’s confidence.  
>>  
>> Regards,  
>>  
>> Alex  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> Alex,  
>>  
>> If you do decide to continue along with the method that I suggested,  
>> I'll join back in. To this point, I see no indication that you have  
>> tried to relate the force to the position for the water runs, which is  
>> my standing suggestion to you.  
>>  
>> Chris.  
>>  
>>  
>>  
  
  
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Re: [gmx-users] Gromacs-4.5 (final) is out!

[Justin A. Lemkul]

Da-Wei Li wrote:

The download link seems wrong on Gromacs webpage.  It links to beta4.



Fixed.

-Justin


dawei

On Wed, Sep 1, 2010 at 4:10 PM, Rossen Apostolov 
mailto:rossen.aposto...@cbr.su.se>> wrote:



It is finally here: *Gromacs-4.5* has been just released
. All critical
issues have been resolved to deliver a stable and powerful package
full of many new features
.

Big thanks to all developers and users who made it happen!

Happy simulating !!!


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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-4.5 (final) is out!

[Da-Wei Li]

The download link seems wrong on Gromacs webpage.  It links to beta4.

dawei

On Wed, Sep 1, 2010 at 4:10 PM, Rossen Apostolov  wrote:

>
> It is finally here: *Gromacs-4.5* has been just 
> released.
> All critical issues have been resolved to deliver a stable and powerful
> package full of many new 
> features.
>
>
> Big thanks to all developers and users who made it happen!
>
> Happy simulating !!!
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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[gmx-users] Newest version of Gromacs 4.5 installation

[Moeed]

Hi,

We are installing the newest version of Gromacs - 4.5 on our cluster
(running CentOS) for parallel purposes. We are also using Openmpi version
1.4. However upon installing Gromacs using the command:


./configure --enable-mpi


we ran into this problem below:


* Seems you are compiling with MPI support. You can install the MPI-
  enabled programs with suffixed names to have both MPI and non-MPI
  versions. This is useful e.g. on supercomputers where you usually
  cannot run MPI-linked programs on the login node.
  Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
  You only need MPI for mdrun, so if you already have non-MPI stuff
  installed you can issue make mdrun; make install-mdrun.

  WARNING:
  There are known problems with some MPI implementations:
 OpenMPI version < 1.4.1
 MVAPICH2 version <= 1.4.1

* On most platforms you can save 10X space with dynamic libraries, although
  the binaries might be less portable. Why not try --enable-shared ?


Does this imply that we must update our current Openmpi version from 1.4 to
1.41 in order for Gromacs to be installed? Also, what are the pros and cons
of using '--enable-shared'?


Thank you for your help.
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[gmx-users] Gromacs-4.5 (final) is out!

[Rossen Apostolov]

It is finally here: *Gromacs-4.5* has been just released 
. All critical 
issues have been resolved to deliver a stable and powerful package full 
of many new features 
.


Big thanks to all developers and users who made it happen!

Happy simulating !!!

-- 
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Re: [gmx-users] LJ potential

[Sai Pooja]

Questions inline...

On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users 
>
>  >
> > Thanks Mark. I have just 2 more queries regarding this.
> >
> *> When using tables for the potential, *
> >
> > 1) For VdW interactions, it it alright to use the topology
> file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies
> LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in the case
> of user defined potentials?
> >
> > I ask this because I get a warning when I try to do the above:
>  > :WARNING 2 [file initffd.top, line 8082]:
> >   Using sigma/epsilon based combination rules with user supplied
> potential
> >   function may produce unwanted results
>
> You will need to take suitable care. grompp will only use the combination
> rules if it cannot find an existing definition for that pair of atomtypes,
> so if you make all the definitions, you should be OK. A good way to test
> that you are on the right track is whether you can produce an energy group +
> table file that will reproduce the result GROMACS gets if you leave it
> alone.
>

Mark I apologize but I did not understand your reply.. let me rephrase the
question(I hope to get it right this time):

In the table syntax... LJ potential uses the functional form with C6 and C12
rather tha sigma and epsilon.

The forcefield files however specify sigma and epsilon for atom pairs.

Now, if I want to use the *sigma and epsilon values in the forcefield file
along with tables for energy calculation *do I need to change the forcefield
files sigma and epsilon parameters to C6 and C12? If not, is there something
else I must do for this to work?




>
>  > 2) If one is interested in using PME for electrostatic interactions but
> with different electrostatic interaction functions for different pairs of
> energygrps, is it alright to specify the simple coulomb function in the user
> defined table and use the PME-User option for coulombtype?
>
>
Probably not. The form of the reciprocal-space PME term presupposes a simple
Coulomb function on all atoms. So did the parameterization of the force
field, so you're already taking your life in your hands :-)

How about a simple coulomb function multiplied by a constant?


Pooja

  > On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham
wrote:
>
>> >
>> >
>> > - Original Message -
>> > From: Sai Pooja 
>> > Date: Monday, August 30, 2010 3:33
>> > Subject: Re: [gmx-users] LJ potential
>> > To: Discussion list for GROMACS users 
>> >
>> > > Hi,
>> > >
>> >
>>  > > I am simulating a system of a protein in water. I am trying to run
>> the simulation with a modified protein-water LJ and coulomb interaction.
>> Since LJ and  coulomb interaction parameters are defined at the atomic level
>> in the forcefield files, I cannot figure out a good way to modify them for
>> protein-water interactions specifically. In other words, I want to modify
>> the protein water interaction without altering protein-protein interaction.
>> >
>> > Right, that's totally different from your first question, which implied
>> only protein and thus intra-molecular interactions. When seeking help, you
>> should make sure you  make a complete description the first time, lest you
>> waste everybody's time and effort. That's easier said than done, but you
>> managed to do it on the second attempt :-)
>> >
>> > GROMACS allows you to use table lookups for non-bonded interactions,
>> and to use different tables for interactions between different energy
>> groups. So your problem reduces to generating the different tables and
>> groups, and assigning tables to pairs of groups. Aspects of this process are
>> discussed in several places in the manual.
>> >
>> > Mark
>>  >
>> >
>> > > On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert <
>> domm...@icp.uni-stuttgart.de> wrote:
>>
>>> > > -BEGIN PGP SIGNED MESSAGE-
>>> > > Hash: SHA1
>>> > >
>>> > > On 08/24/2010 02:27 PM, Sai Pooja wrote:
>>> > > > Hi,
>>> > > >
>>> > > > If there are n types of atoms in protein, how does one specify:
>>> > > > 1) Different types of LJ non-bonded interactions for different
>>> pairs?
>>> > > > 2) Modified Coloumb(by a pre-multiplier) interactions for
>>> different pairs?
>>> > > >
>>> > > > Pooja
>>> > > >
>>> > > >
>>> > >
>>> > > Hi,
>>> > >
>>> > >  this can be defined in the top file. Take a look at the manual
>>> > > regarding the force field and different function types for the
>>> nonbonded
>>> > > interactions. This will surely help.
>>> > >
>>> > > /Flo
>>> > >
>>> > > - --
>>> > > Florian Dommert
>>> > > Dipl.-Phys.
>>> > >
>>> > > Institute for Computational Physics
>>> > >
>>> > > University Stuttgart
>>> > >
>>> > > Pfaffenwaldring 27
>>> > > 70569 Stuttgart
>>> > >
>>> > > Phone: +49(0)711/685-6-3613
>>> > > Fax:   +49-(0)711/685-6-3658
>>> > >
>>> > > EMail: domm...@icp.u

Re: [gmx-users] Replica exchange with multiple tables?

[David van der Spoel]

On 2010-09-01 17.32, Sai Pooja wrote:

Hi,
Does gromacs allow the use of a _different set_ of energy tables for
different replicas? If not, any suggestions on how this can be done?
REM + 'different set of tables for each replica' + 'separate tables for
different pairs of energygroups'
Pooja


This would have to be programmed.

Note that in gromacs the coordinates (boxes) are exchanged, so the 
temperatures are fixed on each node.



On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote:



- Original Message -
From: Sai Pooja mailto:saipo...@gmail.com>>
Date: Tuesday, August 31, 2010 2:45
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>

 >
 > Thanks Mark. I have just 2 more queries regarding this.
 >
*> When using tables for the potential, *
 >
 > 1) For VdW interactions, it it alright to use the topology
file generated by pdb2gmx using a forcefield (eg. CHARMM27) which
specifies LJ paramters as 'sigma' and 'epsilon' instead of C6 and
C12 as in the case of user defined potentials?
 >
 > I ask this because I get a warning when I try to do the above:
 > :WARNING 2 [file initffd.top, line 8082]:
 >   Using sigma/epsilon based combination rules with user supplied
potential
 >   function may produce unwanted results

You will need to take suitable care. grompp will only use the
combination rules if it cannot find an existing definition for that
pair of atomtypes, so if you make all the definitions, you should be
OK. A good way to test that you are on the right track is whether
you can produce an energy group + table file that will reproduce the
result GROMACS gets if you leave it alone.

 > 2) If one is interested in using PME for electrostatic
interactions but with different electrostatic interaction functions
for different pairs of energygrps, is it alright to specify the
simple coulomb function in the user defined table and use the
PME-User option for coulombtype?

Probably not. The form of the reciprocal-space PME term presupposes
a simple Coulomb function on all atoms. So did the parameterization
of the force field, so you're already taking your life in your hands :-)

Mark

 > On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham
 wrote:

 >
 >
 > - Original Message -
 > From: Sai Pooja 
 > Date: Monday, August 30, 2010 3:33
 > Subject: Re: [gmx-users] LJ potential
 > To: Discussion list for GROMACS users 
 >
 > > Hi,
 > >
 >
 > > I am simulating a system of a protein in water. I am trying
to run the simulation with a modified protein-water LJ
and coulomb interaction. Since LJ and  coulomb interaction
parameters are defined at the atomic level in the forcefield
files, I cannot figure out a good way to modify them for
protein-water interactions specifically. In other words, I want
to modify the protein water interaction without
altering protein-protein interaction.
 >
 > Right, that's totally different from your first question,
which implied only protein and thus intra-molecular
interactions. When seeking help, you should make sure you  make
a complete description the first time, lest you waste
everybody's time and effort. That's easier said than done, but
you managed to do it on the second attempt :-)
 >
 > GROMACS allows you to use table lookups for non-bonded
interactions, and to use different tables for interactions
between different energy groups. So your problem reduces to
generating the different tables and groups, and assigning tables
to pairs of groups. Aspects of this process are discussed in
several places in the manual.
 >
 > Mark
 >
 >
 > > On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert
 wrote:

 > > -BEGIN PGP SIGNED MESSAGE-
 > > Hash: SHA1
 > >
 > > On 08/24/2010 02:27 PM, Sai Pooja wrote:
 > > > Hi,
 > > >
 > > > If there are n types of atoms in protein, how does
one specify:
 > > > 1) Different types of LJ non-bonded interactions for
different pairs?
 > > > 2) Modified Coloumb(by a pre-multiplier) interactions
for different pairs?
 > > >
 > > > Pooja
 > > >
 > > >
 > >
 > > Hi,
 > >
 > >  this can be defined in the top file. Take a look at
the manual
 > > regarding the force field and different function types
for the nonbonded
 > > interactions. Th

[gmx-users] Replica exchange with multiple tables?

[Sai Pooja]

Hi,

Does gromacs allow the use of a *different set* of energy tables for
different replicas? If not, any suggestions on how this can be done?

REM + 'different set of tables for each replica' + 'separate tables for
different pairs of energygroups'

Pooja




On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users 
>
>  >
> > Thanks Mark. I have just 2 more queries regarding this.
> >
> *> When using tables for the potential, *
> >
> > 1) For VdW interactions, it it alright to use the topology
> file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies
> LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in the case
> of user defined potentials?
> >
> > I ask this because I get a warning when I try to do the above:
>  > :WARNING 2 [file initffd.top, line 8082]:
> >   Using sigma/epsilon based combination rules with user supplied
> potential
> >   function may produce unwanted results
>
> You will need to take suitable care. grompp will only use the combination
> rules if it cannot find an existing definition for that pair of atomtypes,
> so if you make all the definitions, you should be OK. A good way to test
> that you are on the right track is whether you can produce an energy group +
> table file that will reproduce the result GROMACS gets if you leave it
> alone.
>
>  > 2) If one is interested in using PME for electrostatic interactions but
> with different electrostatic interaction functions for different pairs of
> energygrps, is it alright to specify the simple coulomb function in the user
> defined table and use the PME-User option for coulombtype?
>
> Probably not. The form of the reciprocal-space PME term presupposes a
> simple Coulomb function on all atoms. So did the parameterization of the
> force field, so you're already taking your life in your hands :-)
>
> Mark
>
>  > On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham 
> wrote:
>
>> >
>> >
>> > - Original Message -
>> > From: Sai Pooja 
>> > Date: Monday, August 30, 2010 3:33
>> > Subject: Re: [gmx-users] LJ potential
>> > To: Discussion list for GROMACS users 
>> >
>> > > Hi,
>> > >
>> >
>>  > > I am simulating a system of a protein in water. I am trying to run
>> the simulation with a modified protein-water LJ and coulomb interaction.
>> Since LJ and  coulomb interaction parameters are defined at the atomic level
>> in the forcefield files, I cannot figure out a good way to modify them for
>> protein-water interactions specifically. In other words, I want to modify
>> the protein water interaction without altering protein-protein interaction.
>> >
>> > Right, that's totally different from your first question, which implied
>> only protein and thus intra-molecular interactions. When seeking help, you
>> should make sure you  make a complete description the first time, lest you
>> waste everybody's time and effort. That's easier said than done, but you
>> managed to do it on the second attempt :-)
>> >
>> > GROMACS allows you to use table lookups for non-bonded interactions,
>> and to use different tables for interactions between different energy
>> groups. So your problem reduces to generating the different tables and
>> groups, and assigning tables to pairs of groups. Aspects of this process are
>> discussed in several places in the manual.
>> >
>> > Mark
>>  >
>> >
>> > > On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert <
>> domm...@icp.uni-stuttgart.de> wrote:
>>
>>> > > -BEGIN PGP SIGNED MESSAGE-
>>> > > Hash: SHA1
>>> > >
>>> > > On 08/24/2010 02:27 PM, Sai Pooja wrote:
>>> > > > Hi,
>>> > > >
>>> > > > If there are n types of atoms in protein, how does one specify:
>>> > > > 1) Different types of LJ non-bonded interactions for different
>>> pairs?
>>> > > > 2) Modified Coloumb(by a pre-multiplier) interactions for
>>> different pairs?
>>> > > >
>>> > > > Pooja
>>> > > >
>>> > > >
>>> > >
>>> > > Hi,
>>> > >
>>> > >  this can be defined in the top file. Take a look at the manual
>>> > > regarding the force field and different function types for the
>>> nonbonded
>>> > > interactions. This will surely help.
>>> > >
>>> > > /Flo
>>> > >
>>> > > - --
>>> > > Florian Dommert
>>> > > Dipl.-Phys.
>>> > >
>>> > > Institute for Computational Physics
>>> > >
>>> > > University Stuttgart
>>> > >
>>> > > Pfaffenwaldring 27
>>> > > 70569 Stuttgart
>>> > >
>>> > > Phone: +49(0)711/685-6-3613
>>> > > Fax:   +49-(0)711/685-6-3658
>>> > >
>>> > > EMail: domm...@icp.uni-stuttgart.de
>>> > > Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>> > > -BEGIN PGP SIGNATURE-
>>> > > Version: GnuPG v1.4.10 (GNU/Linux)
>>> > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>> > >
>>> > > iEYEARECAAYFAkxzu7wACgkQLpNNBb9GiPlGAQCghZWQobj9j2SqvYC1gU5e3QR9
>>> > > WVQAnAjv9tZ6xGRhc+S1vSSQh9kek4xZ
>>> > > =T+Yb
>>> > > ---

Re: [gmx-users] Different impacts in the pressure

[Erik Marklund]

 I guess that could be done with mrun -rerun, where you would have to 
rerun with only the interaction you're interested in turned on. Never 
tried it myself though.


Erik

Mikhail Stukan skrev 2010-08-31 15.05:


Dear Gromacs users,

I am quite new in gromacs, so maybe I am missing something obvious.

Is there any standard option/function to calculate different impacts 
into the pressure tensor (i.e. due to VdW interactions, due to bonded 
interaction, due to electrostatics etc.) ?


Thanks a lot in advance,

Mikhail

=

Dr Mikhail Stukan

Schlumberger Dhahran Carbonate Research Center,

Dhahran Techno Valley  - KFUPM,

P.O. Box 39011, Dammam / Doha Camp  31942,

Kingdom of Saudi Arabia

Tel: +966 3 331 0300 ext 6182

Fax:+966 3 330 0845
mstu...@slb.com 




--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] gmx 4.5 and openmm on Mac, still not compiling

[Szilárd Páll]

Hi,

FYI, now building the GPU accelerated version in a non-clean build
tree (used to build the CPU version) should work as well as the other
way around.

_However_, be warned that in the latter case the CPU build-related
parameters do _not_ get reset to their default values (e.g.
GMX_ACCELERATION != auto, GMX_THREADS != on)!

The safest way (and what I strongly recommend) is to have different
build trees for different builds or, as Rossen suggested, just remove
the cache before building something different.

Regards,
--
Szilárd



On Tue, Aug 24, 2010 at 2:39 PM, Rossen Apostolov
 wrote:
>  Hi Alan,
>
> With OpenMM you don't need SSE kernels. If you look at CMakeCache.txt you'll
> see that
>
>
>> Hi there,
>>
>> I've tried before and the error still basically the same (line error in
>> 'nb_kernel400_x86_64_sse.c' was 630, now's 629) .
>>
>> I am using gmx 4.5 release-4-5-patches branch.
>>
>> git pull
>> rm -fr build
>> mkdir -p build
>> cd build
>> cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF ..
>
> Since GMX_OPENMM=OFF, GMX_ACCELERATION is automatically set to SSE.
>>
>> make clean
>
> This command doesn't remove CMaceCache.txt!
>>
>> make -j 2
>> sudo make install # all fine till here
>> make clean
>> export OPENMM_ROOT_DIR=/usr/local/openmm
>> cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON ..
>
> Now GMX_OPENMM is ON, *but* GMX_ACCELERATION is still SSE (the value is read
> from the cache). This is an issue with the cmake system. You should either
> remove CMakeCache.txt or add an explicit -DGMX_ACCELERATION=OFF to the cmake
> command.
>
> This is a workaround at the moment but the issue should be fixed.
>
> Rossen
>>
>> make mdrun
>>
>> [snip]
>> [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o
>> [ 56%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:
>> In function ‘nb_kernel400nf_x86_64_sse’:
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: (Each undeclared identifier is reported only once
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: for each function it appears in.)
>>
>> /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
>> error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)
>> make[3]: ***
>> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o]
>> Error 1
>> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
>> make: *** [mdrun] Error 2
>>
>> Any help would be appreciated.
>>
>> Thanks,
>>
>> Alan
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28 <<
>
> --
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