Re: [gmx-users] .GRO Formatting

[Dr. Vitaly Chaban]

In GRO file, the atom numbers do not really matter. Just use any number you
like. It will work correctly.

mdrun will renumber atoms from 9, as it likes, automatically.

Dr. Vitaly Chaban






On Thu, May 30, 2013 at 4:57 AM, Phil  wrote:

> I'm working on a .GRO file and have come across a formatting error.
>
> In the manual, it states that the spacing for each column in the .GRO file
> is:
>
> residue number (5 positions, integer)
> residue name (5 characters)
> atom name (5 characters)
> atom number (5 positions, integer)
> position (in nm, x y z in 3 columns, each 8 positions with 3 decimal
> places)
> velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
> decimal places)
>
> In my .GRO file, the atom number exceeds 5 positions. How should I reformat
> the .GRO file to account for this?
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/GRO-Formatting-tp5008625.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] .GRO Formatting

[Tsjerk Wassenaar]

Hey,

If the gro file was built with a non-gmx program, it may be that the
numbers indeed broke the format, which then needs to be fixed. In case you
write your own program, you want to use a statement like atid = atid %1e5
to make sure it doesn't go over five digits. Correcting the format is
possible, but may become a tiny bit nasty.

Cheers,

Tsjerk



On Thu, May 30, 2013 at 9:09 AM, Dr. Vitaly Chaban wrote:

> In GRO file, the atom numbers do not really matter. Just use any number you
> like. It will work correctly.
>
> mdrun will renumber atoms from 9, as it likes, automatically.
>
> Dr. Vitaly Chaban
>
>
>
>
>
>
> On Thu, May 30, 2013 at 4:57 AM, Phil  wrote:
>
> > I'm working on a .GRO file and have come across a formatting error.
> >
> > In the manual, it states that the spacing for each column in the .GRO
> file
> > is:
> >
> > residue number (5 positions, integer)
> > residue name (5 characters)
> > atom name (5 characters)
> > atom number (5 positions, integer)
> > position (in nm, x y z in 3 columns, each 8 positions with 3 decimal
> > places)
> > velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
> > decimal places)
> >
> > In my .GRO file, the atom number exceeds 5 positions. How should I
> reformat
> > the .GRO file to account for this?
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/GRO-Formatting-tp5008625.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
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Re: [gmx-users] Vritual Sites and simulation time-step

[Mark Abraham]

Manual 6.7?


On Thu, May 30, 2013 at 7:05 AM, James Starlight wrote:

> Dear Gromacs users!
>
> In some discussions I've noticed that people told about usage of virtual
> sites which allow to increase time step of the simulation of such systems.
> >From manual and tutorial its not quite understand for me how with
> inclusion
> of such dummy atoms (which can be used to reduce number of atoms of the
> some solvent-like molecule or to mimic  electron pairs in the water for
> instance)  influence on time-step can be achieved ?
>
>
> James
> --
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Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

[Mark Abraham]

No charges = no problem. You can trivially test this yourself with mdrun
-rerun ;-)  Manual 4.1.4 talks about what RF is doing.

Mark


On Thu, May 30, 2013 at 6:38 AM, Dallas Warren wrote:

> In a system that has no charges, should we observe a difference between
> simulations using PME/Cut-offs or Reaction Field?
>
> >From my understanding there should not be, since there are no charges
> which treatment you use shouldn't' make a difference.
>
> However, it does and I am trying to work out why.
>
> Any suggestions on the reason?
>
> What is it that Reaction Field is doing, does it influence anything other
> than long range charge interactions?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Vritual Sites and simulation time-step

[James Starlight]

Mark,

thanks for advise. As I understood for the usage of virtual sites in
typical protein-water system I should
(1) define all hydrogens as the virtual atoms  (2) increase  atom masses of
the hydrogens presented in the water, COOH NH2 OH and SH as well as polar
groups (3) make virtual sites for the angles and dihedrals of peptide bond
as well as sidechains.

Also I've noticed that (1) and (2) can be done with the pdb2gmx with
options  -vsite and -heavyh respectfully. From this point its not quite
clear for me
(1) should I make some corrections in topology for dihedrals? In the manual
6.7 I've found some suggestions for the dihedrals of the different
functional groups.
(2) should I define VSITES for solvent  molecules filled into the box by
the genbox ?
(3) As I understood the inclusion of the VSITES for hydrogens would allow
me to increase timestep up to 5-8fs. What possible  negative side-effects
of the inclusion of VSITES might occur in simulation ?

James

2013/5/30 Mark Abraham 

> Manual 6.7?
>
>
> On Thu, May 30, 2013 at 7:05 AM, James Starlight  >wrote:
>
> > Dear Gromacs users!
> >
> > In some discussions I've noticed that people told about usage of virtual
> > sites which allow to increase time step of the simulation of such
> systems.
> > >From manual and tutorial its not quite understand for me how with
> > inclusion
> > of such dummy atoms (which can be used to reduce number of atoms of the
> > some solvent-like molecule or to mimic  electron pairs in the water for
> > instance)  influence on time-step can be achieved ?
> >
> >
> > James
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> >
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[gmx-users] Overlap between PC motions

[Miguel Ángel Mompeán García]

Dear all,

I posted some days ago an issue regarding overlap values. If any of you is
experienced with this I would appreciate some comments. Please find below
the mentioned post:


I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time windows, I expect the overlap to be 1 only when the time
interval is equal to 110ns, since both covariance matrices are identical.
However, I found that from the interval 0-70 forwards (I'm increasing each
window in 10ns) the overlap reaches that value. Is this expected? From the
rmsd, cosine content and visual inspection of the trajectory I expected
small changes from this point till the total time, but not the two matrices
being equal... Am I doing something wrong or this may happen?

Here is my data set of results:

Normalized Shape DT
0.6110.6380-10ns
0.6160.6500-20ns
0.6460.6710-30ns
0.6560.6780-40ns
0.6590.6830-50ns
0.8730.9190-60ns
1.0001.0000-70ns
1.0001.0000-80ns
1.0001.0000-90ns
1.0001.0000-100ns
1.0001.0000-110ns = Ttot


Regards,
Miguel
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Re: [gmx-users] Vritual Sites and simulation time-step

[James Starlight]

Also some questions about corrections in the mdp besides the time-step file
which should be included with the VS.

1) What constrains algorithm should I use ?
typically I use
; Bond parameters
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

2) Should I vary tau_t constant assuming that I use SD integrator as the
thermostat ( I'm using 2 ps ) ?

2013/5/30 James Starlight 

> Mark,
>
> thanks for advise. As I understood for the usage of virtual sites in
> typical protein-water system I should
> (1) define all hydrogens as the virtual atoms  (2) increase  atom masses
> of the hydrogens presented in the water, COOH NH2 OH and SH as well as
> polar groups (3) make virtual sites for the angles and dihedrals of peptide
> bond as well as sidechains.
>
> Also I've noticed that (1) and (2) can be done with the pdb2gmx with
> options  -vsite and -heavyh respectfully. From this point its not quite
> clear for me
> (1) should I make some corrections in topology for dihedrals? In the
> manual 6.7 I've found some suggestions for the dihedrals of the different
> functional groups.
> (2) should I define VSITES for solvent  molecules filled into the box by
> the genbox ?
> (3) As I understood the inclusion of the VSITES for hydrogens would allow
> me to increase timestep up to 5-8fs. What possible  negative side-effects
> of the inclusion of VSITES might occur in simulation ?
>
> James
>
>
> 2013/5/30 Mark Abraham 
>
>> Manual 6.7?
>>
>>
>> On Thu, May 30, 2013 at 7:05 AM, James Starlight > >wrote:
>>
>> > Dear Gromacs users!
>> >
>> > In some discussions I've noticed that people told about usage of virtual
>> > sites which allow to increase time step of the simulation of such
>> systems.
>> > >From manual and tutorial its not quite understand for me how with
>> > inclusion
>> > of such dummy atoms (which can be used to reduce number of atoms of the
>> > some solvent-like molecule or to mimic  electron pairs in the water for
>> > instance)  influence on time-step can be achieved ?
>> >
>> >
>> > James
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
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Re: [gmx-users] Overlap between PC motions

[Tsjerk Wassenaar]

Hi Miguel,

Sorry for not responding earlier, but the question isn't really simple :)
What you do is determining the covariance matrix from the start up to a
certain point and see for different end points what the overlap is with the
covariance matrix from the whole. This means that in all cases, the
relaxation of the system is included, and this is the dominant contribution
to your covariance matrix. At some point, the system has reached the region
around B and then stays there. All kinds of things may be happening, but
they're overwhelmed by the changes associated with the relaxation. Hence,
the part of the trajectory after 70 ns doesn't contribute significantly to
the covariance matrix anymore.

Hope it helps,

Tsjerk



On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García <
mig.momp...@gmail.com> wrote:

> Dear all,
>
> I posted some days ago an issue regarding overlap values. If any of you is
> experienced with this I would appreciate some comments. Please find below
> the mentioned post:
>
>
> I am doing PCA on a 110ns run.
> When calculating the subspace overlap from independent PCA performed in
> different time windows, I expect the overlap to be 1 only when the time
> interval is equal to 110ns, since both covariance matrices are identical.
> However, I found that from the interval 0-70 forwards (I'm increasing each
> window in 10ns) the overlap reaches that value. Is this expected? From the
> rmsd, cosine content and visual inspection of the trajectory I expected
> small changes from this point till the total time, but not the two matrices
> being equal... Am I doing something wrong or this may happen?
>
> Here is my data set of results:
>
> Normalized Shape DT
> 0.6110.6380-10ns
> 0.6160.6500-20ns
> 0.6460.6710-30ns
> 0.6560.6780-40ns
> 0.6590.6830-50ns
> 0.8730.9190-60ns
> 1.0001.0000-70ns
> 1.0001.0000-80ns
> 1.0001.0000-90ns
> 1.0001.0000-100ns
> 1.0001.0000-110ns = Ttot
>
>
> Regards,
> Miguel
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

[Dr. Vitaly Chaban]

Hmmm...

And what does the observed difference look like, numerically?





On Thu, May 30, 2013 at 10:14 AM, Mark Abraham wrote:

> No charges = no problem. You can trivially test this yourself with mdrun
> -rerun ;-)  Manual 4.1.4 talks about what RF is doing.
>
> Mark
>
>
> On Thu, May 30, 2013 at 6:38 AM, Dallas Warren  >wrote:
>
> > In a system that has no charges, should we observe a difference between
> > simulations using PME/Cut-offs or Reaction Field?
> >
> > >From my understanding there should not be, since there are no charges
> > which treatment you use shouldn't' make a difference.
> >
> > However, it does and I am trying to work out why.
> >
> > Any suggestions on the reason?
> >
> > What is it that Reaction Field is doing, does it influence anything other
> > than long range charge interactions?
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Discovery Biology
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.war...@monash.edu
> > +61 3 9903 9304
> > -
> > When the only tool you own is a hammer, every problem begins to resemble
> a
> > nail.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
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Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

[Mark Abraham]

Things should be identical - any quantity computed from a zero charge has
to be zero :-).

Mark

On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban wrote:

> Hmmm...
>
> And what does the observed difference look like, numerically?
>
>
>
>
>
> On Thu, May 30, 2013 at 10:14 AM, Mark Abraham  >wrote:
>
> > No charges = no problem. You can trivially test this yourself with mdrun
> > -rerun ;-)  Manual 4.1.4 talks about what RF is doing.
> >
> > Mark
> >
> >
> > On Thu, May 30, 2013 at 6:38 AM, Dallas Warren  > >wrote:
> >
> > > In a system that has no charges, should we observe a difference between
> > > simulations using PME/Cut-offs or Reaction Field?
> > >
> > > >From my understanding there should not be, since there are no charges
> > > which treatment you use shouldn't' make a difference.
> > >
> > > However, it does and I am trying to work out why.
> > >
> > > Any suggestions on the reason?
> > >
> > > What is it that Reaction Field is doing, does it influence anything
> other
> > > than long range charge interactions?
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Drug Discovery Biology
> > > Monash Institute of Pharmaceutical Sciences, Monash University
> > > 381 Royal Parade, Parkville VIC 3052
> > > dallas.war...@monash.edu
> > > +61 3 9903 9304
> > > -
> > > When the only tool you own is a hammer, every problem begins to
> resemble
> > a
> > > nail.
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
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> > >
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Re: [gmx-users] Overlap between PC motions

[Miguel Ángel Mompeán García]

Hi Tsjerk,

Thanks for the reply! So, let me see if I am getting the things right. The
same fitting structure is used for the overlap calculation. Since the
averaged structure is used for the covariance matrices, this is the reason
why the relaxation is included. Am I right?
The overall behavior of the system is that the structure keeps very
"compact" and one additional hydrogen bond between two residues is formed
at ~60ns, and stable till the end of the run, as computed with g_hbond.
That interaction is already present in the average structure. So if I
understood properly your comment, from the time window 0-70 up to the end,
 there will not be significant contributions to the covariance matrix.

Thanks for your valuable comments. Highly appreciated!


2013/5/30 Tsjerk Wassenaar 

> Hi Miguel,
>
> Sorry for not responding earlier, but the question isn't really simple :)
> What you do is determining the covariance matrix from the start up to a
> certain point and see for different end points what the overlap is with the
> covariance matrix from the whole. This means that in all cases, the
> relaxation of the system is included, and this is the dominant contribution
> to your covariance matrix. At some point, the system has reached the region
> around B and then stays there. All kinds of things may be happening, but
> they're overwhelmed by the changes associated with the relaxation. Hence,
> the part of the trajectory after 70 ns doesn't contribute significantly to
> the covariance matrix anymore.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García <
> mig.momp...@gmail.com> wrote:
>
> > Dear all,
> >
> > I posted some days ago an issue regarding overlap values. If any of you
> is
> > experienced with this I would appreciate some comments. Please find below
> > the mentioned post:
> >
> >
> > I am doing PCA on a 110ns run.
> > When calculating the subspace overlap from independent PCA performed in
> > different time windows, I expect the overlap to be 1 only when the time
> > interval is equal to 110ns, since both covariance matrices are identical.
> > However, I found that from the interval 0-70 forwards (I'm increasing
> each
> > window in 10ns) the overlap reaches that value. Is this expected? From
> the
> > rmsd, cosine content and visual inspection of the trajectory I expected
> > small changes from this point till the total time, but not the two
> matrices
> > being equal... Am I doing something wrong or this may happen?
> >
> > Here is my data set of results:
> >
> > Normalized Shape DT
> > 0.6110.6380-10ns
> > 0.6160.6500-20ns
> > 0.6460.6710-30ns
> > 0.6560.6780-40ns
> > 0.6590.6830-50ns
> > 0.8730.9190-60ns
> > 1.0001.0000-70ns
> > 1.0001.0000-80ns
> > 1.0001.0000-90ns
> > 1.0001.0000-100ns
> > 1.0001.0000-110ns = Ttot
> >
> >
> > Regards,
> > Miguel
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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Re: [gmx-users] Overlap between PC motions

[Tsjerk Wassenaar]

Hi Miguel,

The fitting doesn't play a role; it's the dynamics of the system in the
internal frame. Because the internal frame moves, you fit, so that any
contribution due to the rigid body motion is removed.

For the rest you have to look at it like this: You start out somewhere and
walk (relax) towards some city, several kilometers away. You get there and
get lost in the streets, making random walks. Now, what you do with
covariance analysis is looking at the displacements around the mean
position. Your mean position will lie somewhere between your starting
position and the place where you ended up. The deviations from the mean
will be dominated by vectors pointing from wherever you are in the city
towards your starting point. That will be reflected in the covariance
matrix, which doesn't change much, certainly not in terms of the directions
of the first few eigenvectors.
Probably you're actually more interested in the things you do in the city,
your native configuration energy well. But to analyze that, you have to cut
off the part of the journey that brought you there. So it makes sense to do
the covariance analysis on the last half or quarter of the trajectory. It
would also be interesting to check the convergence from the other side of
the trajectory, varying the starting point of the analysis, rather than the
end point.


Hope it helps,

Tsjerk


On Thu, May 30, 2013 at 1:37 PM, Miguel Ángel Mompeán García <
mig.momp...@gmail.com> wrote:

> Hi Tsjerk,
>
> Thanks for the reply! So, let me see if I am getting the things right. The
> same fitting structure is used for the overlap calculation. Since the
> averaged structure is used for the covariance matrices, this is the reason
> why the relaxation is included. Am I right?
> The overall behavior of the system is that the structure keeps very
> "compact" and one additional hydrogen bond between two residues is formed
> at ~60ns, and stable till the end of the run, as computed with g_hbond.
> That interaction is already present in the average structure. So if I
> understood properly your comment, from the time window 0-70 up to the end,
>  there will not be significant contributions to the covariance matrix.
>
> Thanks for your valuable comments. Highly appreciated!
>
>
> 2013/5/30 Tsjerk Wassenaar 
>
> > Hi Miguel,
> >
> > Sorry for not responding earlier, but the question isn't really simple :)
> > What you do is determining the covariance matrix from the start up to a
> > certain point and see for different end points what the overlap is with
> the
> > covariance matrix from the whole. This means that in all cases, the
> > relaxation of the system is included, and this is the dominant
> contribution
> > to your covariance matrix. At some point, the system has reached the
> region
> > around B and then stays there. All kinds of things may be happening, but
> > they're overwhelmed by the changes associated with the relaxation. Hence,
> > the part of the trajectory after 70 ns doesn't contribute significantly
> to
> > the covariance matrix anymore.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> >
> > On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García <
> > mig.momp...@gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I posted some days ago an issue regarding overlap values. If any of you
> > is
> > > experienced with this I would appreciate some comments. Please find
> below
> > > the mentioned post:
> > >
> > >
> > > I am doing PCA on a 110ns run.
> > > When calculating the subspace overlap from independent PCA performed in
> > > different time windows, I expect the overlap to be 1 only when the time
> > > interval is equal to 110ns, since both covariance matrices are
> identical.
> > > However, I found that from the interval 0-70 forwards (I'm increasing
> > each
> > > window in 10ns) the overlap reaches that value. Is this expected? From
> > the
> > > rmsd, cosine content and visual inspection of the trajectory I expected
> > > small changes from this point till the total time, but not the two
> > matrices
> > > being equal... Am I doing something wrong or this may happen?
> > >
> > > Here is my data set of results:
> > >
> > > Normalized Shape DT
> > > 0.6110.6380-10ns
> > > 0.6160.6500-20ns
> > > 0.6460.6710-30ns
> > > 0.6560.6780-40ns
> > > 0.6590.6830-50ns
> > > 0.8730.9190-60ns
> > > 1.0001.0000-70ns
> > > 1.0001.0000-80ns
> > > 1.0001.0000-90ns
> > > 1.0001.0000-100ns
> > > 1.0001.0000-110ns = Ttot
> > >
> > >
> > > Regards,
> > > Miguel
> > > --
> > > 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.
> > > 

[gmx-users] Increasing performance of siumulation in cluster

[Sainitin Donakonda]

Hi all,

I recently ran 20ns simulation in linux cluster.

Used following script for MD simulation

#This is the first simulation MD.mdp file contains 20 ns setup
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

#This extends 10 ns simulation
tpbconv -s MD_first10.tpr  -o md_extended.tpr -extend 1

mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16


and bsub file

#!/bin/bash
#BSUB -J testgromacs # the job's name/array job
#BSUB -W 120:00   # max. wall clock time in hh:mm
#BSUB -n 16,16  # number of processors Min,Max
#BSUB -o /home/sample/output_%J.log # output file
#BSUB -e /home/sample/errors_%J.log # error file
#BSUB -M 8192 #Memory limit in MB

echo "Started at `date`"
echo

cd /home/sample/

echo "Running gromacs test in `pwd`"

./MD.sh

echo "Finished at `date`"
*
*
*
*
*It ran for total 5 days but didnt give all 20ns simulation ..So i checked
log file for performance *
*Parallel run - timing based on wallclock.*
*
*
*   NODE (s)   Real (s)  (%)*
*   Time: 359019.178 359019.178100.0*
*   4d03h43:39*
*  (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)*
*Performance:445.015 24.708  2.407  9.973*
*
*
*
*
*It looks like this gave very performance 2.4 ns per 9 hours..this looks
very low for me.. Can any body tell me how to increase performance of
simulation*

Thanks

Nitin
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[gmx-users] how to distribute CPU in GPU workstation?

[Albert]

Dear:

 I've got 4 GPU in one GPU workstation. I've submit one of my job by 
command:


mdrun -s md.tpr -gpu_id 01 -n -x md.xtc

I found that all the 24 CPU were occupied by this job. However, I would 
like to submit another job with -gpu_id 23, how should I specify the CPU 
for each job?


thank you very much
best
Albert
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[gmx-users] umbrella sampling for two polymer interaction

[gromacs query]

Dear All,

I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.

I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some distance)

pull= umbrella
pull_geometry   = distance
pull_dim= Y Y Y
pull_start  = ???
pull_ngroups= 2?
pull_group0 = polymer_B
pull_group1 = polymer_A
pull_init1  = 0
pull_rate1  = 0.0


please suggest for following:

1) pull_dim I have set to Y Y Y: Is this correct I do not want to make
it interact with some directional vector

2) Which should be group0 or group1, in other words should I pull both
together or how I should decide which one should be reference and
which to be pulled as both are different polymers?

3) And also what should be pull_ngroups because if there is no
reference group then it should be 2

4) I am not able to understand pull_start option with pull_init1. In
this case if it is set to yes and 0.0 respectively then does that mean
this combination is equivalent to pull_start = No if I just assume
pull_init1 does not have any default value (which is 0.0); not
existing

5) Also finally where are upper and lower bounds defined. pull_k1 =
1000 is harmonic applied to some equilibrium distance value. How this
distance is taken by the programme (or it is just the starting
distance taken between two groups) and what are the +/- values
defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is
assumed equilibrium value and r1 is lower and r4 is upper value which
defines shape of potential)


thanks,

Jiom
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[gmx-users] Re: initial temperature ridiculously high

[Valentina]

Hi Guozhen,

I know it has been a while, BUT I am having same/similar problem with
CLAYFF. I start with a configuration optimised by CASTEP.

Have you found a solution? Did you continue using CLAYFF? I have a ClayFF.ff
available, if you want to compare.

Thanks,V



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[gmx-users] About Compiler Option

[vidhya sankar]

Dear Justin and other gromacs users ,
                                                                    Thank you 
for your Previous reply
I  Have AMD Block Edition FX8350 Processor  Also I have Ubuntu 10.04 OS 



Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, 
which is better)

As you mailed me for the aforesaid about performance
I want to Ugrade gcc version 4.7.2
already i had version gcc 4.4.3 When I want to Upgrade
 
But Though  I give the following Commands


add-apt-repository ppa:ubuntu-toolchain-r/test
apt-get update

apt-get install gcc-4.7
  it has not been updated
this is confirmed When i check gcc version in terminal 

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Re: [gmx-users] About Compiler Option

[Erik Marklund]

"gcc" is probably still your old version. The new one would probably be called 
"gcc-4.7" or similar.

Erik
 
On 30 May 2013, at 15:15, vidhya sankar  wrote:

> Dear Justin and other gromacs users ,
> Thank you 
> for your Previous reply
> I  Have AMD Block Edition FX8350 Processor  Also I have Ubuntu 10.04 OS 
> 
> 
> 
> Using 8 MPI threads
> Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, 
> which is better)
> 
> As you mailed me for the aforesaid about performance
> I want to Ugrade gcc version 4.7.2
> already i had version gcc 4.4.3 When I want to Upgrade
>  
> But Though  I give the following Commands
> 
> 
> add-apt-repository ppa:ubuntu-toolchain-r/test
> apt-get update
> 
> apt-get install gcc-4.7
>   it has not been updated
> this is confirmed When i check gcc version in terminal 
> 
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[gmx-users] GROMACS 4.6.2 released

[Mark Abraham]

Hi GROMACS users,


GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
simulation performance enhancements and some documentation updates. We
encourage all users to upgrade their installations from 4.6 and 4.6.1.


You can find the code, manual, release notes, installation instructions and
test
suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x
http://www.gromacs.org/Documentation/Installation_Instructions
http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz

Happy simulating!


The GROMACS development team
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Re: [gmx-users] GROMACS 4.6.2 released

[Albert]

it seems that Gromacs update quite frequently these days..




On 05/30/2013 05:42 PM, Mark Abraham wrote:

Hi GROMACS users,


GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
simulation performance enhancements and some documentation updates. We
encourage all users to upgrade their installations from 4.6 and 4.6.1.


You can find the code, manual, release notes, installation instructions and
test
suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz
ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x
http://www.gromacs.org/Documentation/Installation_Instructions
http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz

Happy simulating!


The GROMACS development team


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Aw: [gmx-users] umbrella sampling for two polymer interaction

[lloyd riggs]

Dear Jiom,

 

Look at justines tutorial, there's example pull .mdp.

 

Stephan Watkins

 

Gesendet: Donnerstag, 30. Mai 2013 um 14:44 Uhr
Von: "gromacs query" 
An: "Discussion list for GROMACS users" 
Betreff: [gmx-users] umbrella sampling for two polymer interaction

Dear All,

I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.

I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some distance)

pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = ???
pull_ngroups = 2?
pull_group0 = polymer_B
pull_group1 = polymer_A
pull_init1 = 0
pull_rate1 = 0.0


please suggest for following:

1) pull_dim I have set to Y Y Y: Is this correct I do not want to make
it interact with some directional vector

2) Which should be group0 or group1, in other words should I pull both
together or how I should decide which one should be reference and
which to be pulled as both are different polymers?

3) And also what should be pull_ngroups because if there is no
reference group then it should be 2

4) I am not able to understand pull_start option with pull_init1. In
this case if it is set to yes and 0.0 respectively then does that mean
this combination is equivalent to pull_start = No if I just assume
pull_init1 does not have any default value (which is 0.0); not
existing

5) Also finally where are upper and lower bounds defined. pull_k1 =
1000 is harmonic applied to some equilibrium distance value. How this
distance is taken by the programme (or it is just the starting
distance taken between two groups) and what are the +/- values
defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is
assumed equilibrium value and r1 is lower and r4 is upper value which
defines shape of potential)


thanks,

Jiom
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Re: [gmx-users] umbrella sampling for two polymer interaction

[gromacs query]

Dear Lloyd,

I have read that but my system is different

regards,


On Thu, May 30, 2013 at 8:28 PM, lloyd riggs  wrote:

> Dear Jiom,
>
> Look at justines tutorial, there's example pull .mdp.
>
> Stephan Watkins
>
> *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr
> *Von:* "gromacs query" 
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* [gmx-users] umbrella sampling for two polymer interaction
> Dear All,
>
> I want to do Umbrella sampling between two different polymers (A and B)
> interacting with each other with starting configuration separated by some
> distance and I am trying to bring them closer.
>
> I have some queries regarding pull inputs: (this is for to run a umbrella
> sampling at some distance)
>
> pull = umbrella
> pull_geometry = distance
> pull_dim = Y Y Y
> pull_start = ???
> pull_ngroups = 2?
> pull_group0 = polymer_B
> pull_group1 = polymer_A
> pull_init1 = 0
> pull_rate1 = 0.0
>
>
> please suggest for following:
>
> 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make
> it interact with some directional vector
>
> 2) Which should be group0 or group1, in other words should I pull both
> together or how I should decide which one should be reference and
> which to be pulled as both are different polymers?
>
> 3) And also what should be pull_ngroups because if there is no
> reference group then it should be 2
>
> 4) I am not able to understand pull_start option with pull_init1. In
> this case if it is set to yes and 0.0 respectively then does that mean
> this combination is equivalent to pull_start = No if I just assume
> pull_init1 does not have any default value (which is 0.0); not
> existing
>
> 5) Also finally where are upper and lower bounds defined. pull_k1 =
> 1000 is harmonic applied to some equilibrium distance value. How this
> distance is taken by the programme (or it is just the starting
> distance taken between two groups) and what are the +/- values
> defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is
> assumed equilibrium value and r1 is lower and r4 is upper value which
> defines shape of potential)
>
>
> thanks,
>
> Jiom
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Re: [gmx-users] GROMACS 4.6.2 released

[rajat desikan]

Excellent work. Thank you all for working so hard!


On Thu, May 30, 2013 at 9:24 PM, Albert  wrote:

> it seems that Gromacs update quite frequently these days..
>
>
>
>
>
> On 05/30/2013 05:42 PM, Mark Abraham wrote:
>
>> Hi GROMACS users,
>>
>>
>> GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
>> simulation performance enhancements and some documentation updates. We
>> encourage all users to upgrade their installations from 4.6 and 4.6.1.
>>
>>
>> You can find the code, manual, release notes, installation instructions
>> and
>> test
>> suite at the links below.
>>
>> ftp://ftp.gromacs.org/pub/**gromacs/gromacs-4.6.2.tar.gz
>> ftp://ftp.gromacs.org/pub/**manual/manual-4.6.2.pdf
>> http://www.gromacs.org/About_**Gromacs/Release_Notes/**Versions_4.6.2.x
>> http://www.gromacs.org/**Documentation/Installation_**Instructions
>> http://gromacs.googlecode.com/**files/regressiontests-4.6.2.**tar.gz
>>
>> Happy simulating!
>>
>>
>> The GROMACS development team
>>
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] Free energy calculation: merge the topology of 2 molecules

[Dejun Lin]

Hi all,

I'm trying to set-up a free energy calculation where a molecule has +2
charge in it's native state (state A) and no charge in the mutant (state
B). Since the molecule has net +2 charge, I have to add counter-ions to
neutralize the system in state A. But in order to transform it to state B
and still maintain a neutral system, the counter-ions have to be
transformed too. I tried only transforming only the target molecule not the
ions but the simulation crashes very quickly.

I searched the gmx-users archives and found some suggestion about merging
the topology definition of ions into that of the molecule under one
[moleculetype] section. I tried that but mdrun warned me with tons of
"inconsistent shift":

There were 2 inconsistent shifts. Check your topology
There were 18 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
There were 12 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
...

and the simulation can't be run in parallel because mdrun would just quick
and complain about not being able to do domain decomposition:

There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 29.6188 nm

I guess the issue is Gromacs thinks those counter-ions belongs chemically
to the target molecule although they are actually not in close proximity in
space, which mess up the DD. partition.

I wonder if there's a way to get around that.

Thanks,
Dejun
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Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules

[lloyd riggs]

I've had 2 problems like this.  1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked,
there might be better suggestions though.

 

Stephan

 

Gesendet: Donnerstag, 30. Mai 2013 um 20:48 Uhr
Von: "Dejun Lin" 
An: gmx-users@gromacs.org
Betreff: [gmx-users] Free energy calculation: merge the topology of 2 molecules

Hi all,

I'm trying to set-up a free energy calculation where a molecule has +2
charge in it's native state (state A) and no charge in the mutant (state
B). Since the molecule has net +2 charge, I have to add counter-ions to
neutralize the system in state A. But in order to transform it to state B
and still maintain a neutral system, the counter-ions have to be
transformed too. I tried only transforming only the target molecule not the
ions but the simulation crashes very quickly.

I searched the gmx-users archives and found some suggestion about merging
the topology definition of ions into that of the molecule under one
[moleculetype] section. I tried that but mdrun warned me with tons of
"inconsistent shift":

There were 2 inconsistent shifts. Check your topology
There were 18 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
There were 12 inconsistent shifts. Check your topology
There were 16 inconsistent shifts. Check your topology
...

and the simulation can't be run in parallel because mdrun would just quick
and complain about not being able to do domain decomposition:

There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 29.6188 nm

I guess the issue is Gromacs thinks those counter-ions belongs chemically
to the target molecule although they are actually not in close proximity in
space, which mess up the DD. partition.

I wonder if there's a way to get around that.

Thanks,
Dejun
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[gmx-users] AMBER99sb-ILDN charges for C-terminus GLY with COOH capping

[santanu roy]

Hello all,

I am using pdb2gmx (4.5.5 version) to create an AMBER99sb-ILDN topology
file for a peptide. It gives me only NH3+ as the N-terminus and COO- as the
C-terminus. But, I want to have the C-terminus as COOH. The C-terminal
residue is GLY.

Can anybody give me some idea how to get the GLY COOH C-terminus using this
force-field? What could be the charges for the terminus?

Thanks a lot,
Santanu
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Re: [gmx-users] GROMACS 4.6.2 released

[Mark Abraham]

On Thu, May 30, 2013 at 5:54 PM, Albert  wrote:

> it seems that Gromacs update quite frequently these days..


We try, thanks! :-) The idea is to get these patch releases out
more-or-less monthly. This time, we spent several weeks noticing various
correctness problems with not-quite-mainstream uses of mdrun that dragged
on longer than we initially thought, else you'd have had it sooner. Thanks
to all the loyal developers, bug fixers and reviewers, too!

Mark
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[gmx-users] Re: GROMACS 4.6.2 released

[Mark Abraham]

Sorry, the link to the release notes should be
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.2

(Darn, I was hoping for a clean sheet, but at least this time we got to
four hours before someone noticed something was wrong!)

Mark


On Thu, May 30, 2013 at 5:42 PM, Mark Abraham wrote:

> Hi GROMACS users,
>
>
> GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some
> simulation performance enhancements and some documentation updates. We
> encourage all users to upgrade their installations from 4.6 and 4.6.1.
>
>
> You can find the code, manual, release notes, installation instructions
> and test
> suite at the links below.
>
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz
> ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x
> http://www.gromacs.org/Documentation/Installation_Instructions
> http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz
>
> Happy simulating!
>
>
> The GROMACS development team
>
>
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Re: [gmx-users] Free energy calculation: merge the topology of 2 molecules

[Dejun Lin]

Thanks for your reply, Stephan.

Did the molecule you worked with have any atoms that are isolated
(non-bonded) to the others?
Was the equilibration run in your 1st case just a way to recruit those
isolated atoms to the others in the same molecule? I suspect I might need
to add artificial bond to connect the counter-ions to the target molecule.

In the 2nd case you mentioned, I'm not sure why it would work for you but
not me because I essentially have every atoms in their single charge groups.

Thanks,
Dejun


2013/5/30 lloyd riggs 

> I've had 2 problems like this.  1 was solved by doing all eq to a good
> degree first in one thread, then the domain decomposition worked in 8 or
> 16...the secound I had to break down the charge groups in the .itp (cg)
> into smaller charge groups and it worked,
> there might be better suggestions though.
>
> Stephan
>
> *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr
> *Von:* "Dejun Lin" 
> *An:* gmx-users@gromacs.org
> *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2
> molecules
> Hi all,
>
> I'm trying to set-up a free energy calculation where a molecule has +2
> charge in it's native state (state A) and no charge in the mutant (state
> B). Since the molecule has net +2 charge, I have to add counter-ions to
> neutralize the system in state A. But in order to transform it to state B
> and still maintain a neutral system, the counter-ions have to be
> transformed too. I tried only transforming only the target molecule not the
> ions but the simulation crashes very quickly.
>
> I searched the gmx-users archives and found some suggestion about merging
> the topology definition of ions into that of the molecule under one
> [moleculetype] section. I tried that but mdrun warned me with tons of
> "inconsistent shift":
>
> There were 2 inconsistent shifts. Check your topology
> There were 18 inconsistent shifts. Check your topology
> There were 16 inconsistent shifts. Check your topology
> There were 12 inconsistent shifts. Check your topology
> There were 16 inconsistent shifts. Check your topology
> ...
>
> and the simulation can't be run in parallel because mdrun would just quick
> and complain about not being able to do domain decomposition:
>
> There is no domain decomposition for 16 nodes that is compatible with the
> given box and a minimum cell size of 29.6188 nm
>
> I guess the issue is Gromacs thinks those counter-ions belongs chemically
> to the target molecule although they are actually not in close proximity in
> space, which mess up the DD. partition.
>
> I wonder if there's a way to get around that.
>
> Thanks,
> Dejun
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RE: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

[Dallas Warren]

Yes, that is what i thought too.

I have one or two things to check, then will report my results.

I have been calculating latent heat of vaporisation for a series of alkanes, 
and the answer is different.  Been trying to work out why, if dime setting are 
wrong etc. Will post my results early next week.

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.j.abra...@gmail.com]
Sent: 30 May 2013 21:31
To: Vitaly Chaban; Discussion list for GROMACS users
Subject: Re: [gmx-users] Difference between the electrostatic treatments
PME/Cut-offs and Reaction Field

Things should be identical - any quantity computed from a zero charge has
to be zero :-).

Mark

On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban wrote:

> Hmmm...
>
> And what does the observed difference look like, numerically?
>
>
>
>
>
> On Thu, May 30, 2013 at 10:14 AM, Mark Abraham  >wrote:
>
> > No charges = no problem. You can trivially test this yourself with mdrun
> > -rerun ;-)  Manual 4.1.4 talks about what RF is doing.
> >
> > Mark
> >
> >
> > On Thu, May 30, 2013 at 6:38 AM, Dallas Warren  > >wrote:
> >
> > > In a system that has no charges, should we observe a difference between
> > > simulations using PME/Cut-offs or Reaction Field?
> > >
> > > >From my understanding there should not be, since there are no charges
> > > which treatment you use shouldn't' make a difference.
> > >
> > > However, it does and I am trying to work out why.
> > >
> > > Any suggestions on the reason?
> > >
> > > What is it that Reaction Field is doing, does it influence anything
> other
> > > than long range charge interactions?
> > >
> > > Catch ya,
> > >
> > > Dr. Dallas Warren
> > > Drug Discovery Biology
> > > Monash Institute of Pharmaceutical Sciences, Monash University
> > > 381 Royal Parade, Parkville VIC 3052
> > > dallas.war...@monash.edu
> > > +61 3 9903 9304
> > > -
> > > When the only tool you own is a hammer, every problem begins to
> resemble
> > a
> > > nail.
> > > --
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[gmx-users] query on replica exchange

[Sanku M]

Hi,
  I am wondering if there is a way I can use twice more number of replica than 
the number of CPU is available so that each replica will run at 50 % CPU 
usage..For example if I have 48 replica and have 24 CPUs, is it a possibility 
to perform Replica exchange in gromacs ?
I was using gromacs4.5.4 and I could not get it worked. It works only when I 
had atleast equal number of Replica and CPU available.
Any help will be appreciated.
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