Re: [gmx-users] gmx spatial error

[Dallas Warren]

Get more memory or process a smaller amount (atoms or trajectory).

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#out-of-memory-when-allocating

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 12 Dec 2019 at 21:24, Apramita Chand 
wrote:

> Dear All,
> I'm coming across the error "Failed to calloc -9223372036854775808 elements
> of size 8 for bin" while running gmx spatial.
> I have three four systems and for the others -nab option with 100 worked
> fine but here, even after increasing -nab to 1000 , it shows insufficient
> memory.
>
> What could be done?
>
> Thanks,
> Apramita
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[gmx-users] gmx spatial error

[Apramita Chand]

Dear All,
I'm coming across the error "Failed to calloc -9223372036854775808 elements
of size 8 for bin" while running gmx spatial.
I have three four systems and for the others -nab option with 100 worked
fine but here, even after increasing -nab to 1000 , it shows insufficient
memory.

What could be done?

Thanks,
Apramita
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[gmx-users] gmx spatial producing negative isodensities.

[Stefan Hansen]

Dear all,

I have been attempting to obtain SDFs using gmx spatial however with the
results of getting negative isodensities. The trajectory contains 25000
frames, and ~1 atoms.

Running gmx spacial with: gmx spatial -s mol_packed.gro -f mol.xtc -bin 0.1
and choosing the co-solute of interest to generate the SDF for and choosing
the system for group to output coords, yielded  the following:

Counts per frame in all 160380 cubes divided by -7.881814e-02
Normalized data: average 1.00e+00, min -0.00e+00, max -2.103577e+00

This test was conducted on 2 different machines 1 using gromacs version
2018.2 and second 2016.3.

Further we found that conducting the very same analysis however using a bin
size of 0.14 yields reasonable results, here meaning postive isodensities.

So my questions are:
Has this behaviour been observed before? i.e. is this a bug?
Am I using the gmx spatial wrong?

Regards,
Stefan
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Re: [gmx-users] gmx spatial

[Dallas Warren]

I would look at what you are using for the reference atoms around
which the SDF is generated. Ideally they should be relatively rigid in
position relative to each other, otherwise the SDF doesn't make as
much sense.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 June 2017 at 16:57, Valerio Ferrario  wrote:
> Yes, you are right, but the problem is that if I visualize the trajectory I
> have the solute around the protein whereas with the spatial distribution
> function I obtain density function around the protein as well as within the
> protein core and this make no sense or at least is not convincing. Moreover
> the trajectory seems very good, with the protein perfectly superposed and
> with the same orientation in each trajectory step. Is there a way to define
> the interaction? i.e. the 2 selected groups interacts when they are within
> a given distance?
>
> Best,
> Valerio
>
> 2017-06-28 3:29 GMT+02:00 Dallas Warren :
>
>> The values for the isosurface are a probability, just like for an RDF,
>> so negative values don't make any sense.
>>
>> Visualise the trajectory you are analysing to see how the solute moves
>> around, and get a visual idea of if the SDF generated is consistent
>> with what you are seeing.
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.war...@monash.edu
>> -
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
>>
>> On 28 June 2017 at 01:45, Valerio Ferrario 
>> wrote:
>> > Dear Users,
>> >
>> > I am trying to use the gmx spatial tool in order to understand how a
>> solute
>> > interact with the protein. I performed the calculation following all the
>> > instructions (including the 2 trjconv steps). The trajectory obtained
>> looks
>> > fine, and I calculated the sdf with the following command:
>> >
>> > gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx
>> >
>> > and selecting the protein and an atom of my solute molecules (in the
>> index)
>> >
>> > but when I open the grid.cube file with vmd and I visualize it as
>> > isosurface I have the density function even within the protein core... I
>> > thought that the density should be just around the protein (in this
>> case).
>> > Moreover I have just positive values for the isosurface, is that normal?
>> Am
>> > I doing something wrong?
>> >
>> > Thanks a lot,
>> > Valerio Ferrario
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> >
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>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
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>>
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Re: [gmx-users] gmx spatial

[Valerio Ferrario]

Yes, you are right, but the problem is that if I visualize the trajectory I
have the solute around the protein whereas with the spatial distribution
function I obtain density function around the protein as well as within the
protein core and this make no sense or at least is not convincing. Moreover
the trajectory seems very good, with the protein perfectly superposed and
with the same orientation in each trajectory step. Is there a way to define
the interaction? i.e. the 2 selected groups interacts when they are within
a given distance?

Best,
Valerio

2017-06-28 3:29 GMT+02:00 Dallas Warren :

> The values for the isosurface are a probability, just like for an RDF,
> so negative values don't make any sense.
>
> Visualise the trajectory you are analysing to see how the solute moves
> around, and get a visual idea of if the SDF generated is consistent
> with what you are seeing.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 28 June 2017 at 01:45, Valerio Ferrario 
> wrote:
> > Dear Users,
> >
> > I am trying to use the gmx spatial tool in order to understand how a
> solute
> > interact with the protein. I performed the calculation following all the
> > instructions (including the 2 trjconv steps). The trajectory obtained
> looks
> > fine, and I calculated the sdf with the following command:
> >
> > gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx
> >
> > and selecting the protein and an atom of my solute molecules (in the
> index)
> >
> > but when I open the grid.cube file with vmd and I visualize it as
> > isosurface I have the density function even within the protein core... I
> > thought that the density should be just around the protein (in this
> case).
> > Moreover I have just positive values for the isosurface, is that normal?
> Am
> > I doing something wrong?
> >
> > Thanks a lot,
> > Valerio Ferrario
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] gmx spatial

[Dallas Warren]

The values for the isosurface are a probability, just like for an RDF,
so negative values don't make any sense.

Visualise the trajectory you are analysing to see how the solute moves
around, and get a visual idea of if the SDF generated is consistent
with what you are seeing.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 June 2017 at 01:45, Valerio Ferrario  wrote:
> Dear Users,
>
> I am trying to use the gmx spatial tool in order to understand how a solute
> interact with the protein. I performed the calculation following all the
> instructions (including the 2 trjconv steps). The trajectory obtained looks
> fine, and I calculated the sdf with the following command:
>
> gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx
>
> and selecting the protein and an atom of my solute molecules (in the index)
>
> but when I open the grid.cube file with vmd and I visualize it as
> isosurface I have the density function even within the protein core... I
> thought that the density should be just around the protein (in this case).
> Moreover I have just positive values for the isosurface, is that normal? Am
> I doing something wrong?
>
> Thanks a lot,
> Valerio Ferrario
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] gmx spatial

[Valerio Ferrario]

Dear Users,

I am trying to use the gmx spatial tool in order to understand how a solute
interact with the protein. I performed the calculation following all the
instructions (including the 2 trjconv steps). The trajectory obtained looks
fine, and I calculated the sdf with the following command:

gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx

and selecting the protein and an atom of my solute molecules (in the index)

but when I open the grid.cube file with vmd and I visualize it as
isosurface I have the density function even within the protein core... I
thought that the density should be just around the protein (in this case).
Moreover I have just positive values for the isosurface, is that normal? Am
I doing something wrong?

Thanks a lot,
Valerio Ferrario
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[gmx-users] gmx spatial

[Christopher Neale]

Dear Hoda:

You’re likely seeing water mostly on one side because of PBC. I suggest you 
modify your commands such that you create a new .gro file in which the protein 
is centred and PBC is re-imaged (trjconv -center -pbc mol) and then use that to 
create a new .tpr file and then use that new .tpr file as input for the -s 
option in your protein fitting (while also using -pbc mol in that command)

I don’t know why you want to remove nonbonded water around the protein 
(Actually, I don’t know what is not nonbonded water…). If you mean you want the 
SDF of only the first hydration shell, then you can use gmx select to output 
particular water molecules and then (since I think you will need to have a 
contant number of waters) you can do some scripting to reset the coordinates of 
all other water molecules to 9 9 9 or something like that (though this may have 
-nab implications during gmx spatial).

Chris.

— original message —

I made Spatial distribution function of water around my enzyme, and I got a
grid.cube file, when I visualize my output file with VMD I see that water
distribution has tendency to one side of enzyme, it means when I change
isovalue in VMD the water molecules increase or decrease from one side of
enzyme but at last they cover whole the enzyme, here is two question:
1. are my commands and choices true?

echo 12 q | gmx_mpi make_ndx -f md_0_1.gro -o indexp.ndx   (12=water)

echo 0 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_S.xtc
-boxcenter tric -ur compact -pbc none (0=system)

echo 4 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_S.xtc -o protein_fit.xtc
-fit rot+trans (4=backbone of protein , 0=system)

echo 12 1 | gmx_mpi spatial -s md_0_1.tpr -f protein_fit.xtc -n indexp.ndx
-nab 300 -bin 0.1 (12=water, 1=protein)

2. how can I remove nonbonded water aroun the protein?

I greatly appreciate your kind consideration and very much look forward to
hearing from you at your earliest convenience.

Best regards,

Hoda
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[gmx-users] gmx spatial

[Hoda Alibiglou]

Dear gmx users,

I made Spatial distribution function of water around my enzyme, and I got a
grid.cube file, when I visualize my output file with VMD I see that water
distribution has tendency to one side of enzyme, it means when I change
isovalue in VMD the water molecules increase or decrease from one side of
enzyme but at last they cover whole the enzyme, here is two question:
1. are my commands and choices true?

echo 12 q | gmx_mpi make_ndx -f md_0_1.gro -o indexp.ndx   (12=water)

echo 0 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_S.xtc
-boxcenter tric -ur compact -pbc none (0=system)

echo 4 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_S.xtc -o protein_fit.xtc
-fit rot+trans (4=backbone of protein , 0=system)

echo 12 1 | gmx_mpi spatial -s md_0_1.tpr -f protein_fit.xtc -n indexp.ndx
-nab 300 -bin 0.1 (12=water, 1=protein)

2. how can I remove nonbonded water aroun the protein?

I greatly appreciate your kind consideration and very much look forward to
hearing from you at your earliest convenience.

Best regards,

Hoda
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