Re: [gmx-users] VMD

[jkrieger]

Hi Rahul,

VMD ran out of memory. Try using trjconv to create a new xtc with a subset
of atoms or a subset of frames.

Best wishes
James

> I tried to visualize my xtc on VMD and the job get killed at 7000 frames
>
> why is that so?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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[gmx-users] VMD

[RAHUL SURESH]

I tried to visualize my xtc on VMD and the job get killed at 7000 frames

why is that so?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] dihedral MM scan

[Mohsen Ramezanpour]

Hi Justin,

Sorry, I am just doing some dihedral population analysis to see which part
is wrong.
I agree. Most likely I am making some mistakes which is hidden to my eyes.
I will prepare and share those with you with the result of population
analysis when prepared.

Cheers
Mohsen

On Thu, Jan 19, 2017 at 7:48 PM, Justin Lemkul  wrote:

>
>
> On 1/19/17 9:40 PM, Mohsen Ramezanpour wrote:
>
>> Thanks Justin,
>>
>> I did the scan for the whole range from -180 to 180 in 10 intervals.
>> I used emtol = 50, and restrain force of 10 to have a better
>> relaxation
>> and restraining, respectively.
>> Unfortunately, my MM profiles do not look similar to GAAMP QM or MM
>> profiles, although I have used the suggested parameters.
>>
>> To check the method I am using and the parameters in the .mdp files, I did
>> the MM scanning on a rotatable bond (CH2-CH2-CH2-CH3) similar to one can
>> be
>> found in a lipid tail.
>> This dihedral was detected as a soft dihedral by GAAMP and there was a
>> good
>> agreement between QM and MM profiles.
>> Here again, my MM profile from scanning does not seem reasonable.
>> Most importantly, there is a very large barrier at angle 0 (ca. 300 times
>> of energies in other angles). Besides, there are sudden increase or
>> decrease in energy just by 10 degree of rotation.
>>
>> Any suggestion is appreciated in advance.
>>
>
> There's really nothing I can suggest without actually seeing the files
> (plots of the energy, the QM inputs and your topology).  Something is
> inconsistent but it's not clear what.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Dihedral Population Analysis -Index file

[Mohsen Ramezanpour]

Thanks Mark. That is great.

I tried that and I made an Index file of what I want.

"DIH" resname DOPC and atomname O  C12  C23  C


However, looking at index files, the order of atom numbers is not right and
give me a wrong dihedral for analysis with g_angle.

8101  8116  8117 8126


*I want it to be like:*
*8117  8116   8126   8101*  (based on atom numbers in the .gro file)
because the order matters for the dihedrals.

So, I used the following one but it did not work neither:
"DIH" resname DOPC and atomname O  C12  C23  C  permute 1  2  3  4
To keep them in the order they are (I assumed 1, 2, 3, 4 represents the
position of atom names in command), and the out put is again:

8101 8116 8117 8126 which is wrong again.

If I assume that the numbers are the positions for atom numbers (not the
atomnames), then 1 would be for 8101, 2 for 8116, 3 for 8117, and 4 for 8126
"DIH" resname DOPC and atomname O  C12  C23  C  permute  3  2  4  1

and the output will be:
8126 8116 8101 8117

Which is not what I want.
Could you please clarify how to make the order as I want?
I read but could not figure it out.

Thanks.


On Tue, Jan 24, 2017 at 3:56 AM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, Jan 24, 2017 at 12:35 AM Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I have a trajectory file which I wish to do a dihedral analysis for
> > specific dihedral.
> > Based on what I understood from mailing list and manual, I made an
> > index.ndx manually for the dihedral of interest in the molecule.
> >
> > Usually, when we make an index file, say for atom P in the system,
> make_ndx
> > makes an index file which includes the numbers for all the P atom in the
> > system. These numbers are the index numbers in the .gro file for the
> whole
> > system.
> >
> > In my index file, I made it based on the atom numbers in the topology
> file
> > for the lipid.
> >
>
> That forces you to use a trajectory file that contains only a single lipid.
> With suitable index groups (for which I recommend gmx select), there's no
> need to do that.
>
>
> > For doing analysis, I first used trjconv and saved only the .xtc file for
> > only the lipid of interest, and then used g_angle to calculate the
> dihedral
> > population. I think what I get is only for ONE lipid over time NOT an
> > average over time and lipids in the system.
> >
>
> Perforce. You only gave gmx angle one lipid and used an index group with
> one dihedral. Whether you got a time series, an average or a distribution
> depends on what you did with gmx angle.
>
>
> > The obvious solution would be to include all the dihedrals for all the
> > lipids in it.
> > BUT, this is not easy to do manually. I tried mk_angndx but it is not
> > giving me what I want.
> > Is there any way to do this?
> >
>
> Sure, see
> http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html
>
> Something along the lines of
>
> resname POPC and name C2 C3 C4 C5
>
> will produce a group that has that dihedral from every POPC.
>
> Mark
>
>
> > Thanks in advance for any comment and suggestion
> >
> > Cheers
> > Mohsen
> >
> > --
> > *Rewards work better than punishment ...*
> > --
> > Gromacs Users mailing list
> >
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[gmx-users] Excluded Volume Effect

[atanu das]

Hi All,
I want to calculate the excluded volume effect on a protein's dynamics from a 
protein-in-water trajectory. I used the following command to calculate the 
volume 
g_sas -s md.tpr -f md.trr -tv volume.xvg -probe 0
The output file (volume.xvg) has 3 columns - 1st column is time, 2nd column is 
volume, and 3rd column is density. Does the volume calculated by the above 
program using probe radius of zero signify the excluded volume? If not, is 
there any other way by which excluded volume can be calculated?
ThanksAtanu    
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Re: [gmx-users] velocity generation in Gromacs 2016

[Justin Lemkul]

On 1/24/17 10:42 AM, Kukol, Andreas wrote:

Hello,

I always used to generate velocities for an MD run in the equilibation step by 
setting
gen-velyes
in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not 
set. Does it mean velocities are now generated by default ?

http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#mdp

The reason behind my question is, I actually forgot to set it and the 
MD-simulation seemed to run normally.



The default is to not generate velocities, which has been the default for many 
years.


http://manual.gromacs.org/documentation/2016.1/user-guide/mdp-options.html#velocity-generation

So your simulation will start out at 0 K and the thermostat will try to bring it 
up to the correct temperature, unless the input coordinate file has velocities 
(e.g. in a .gro file).  You can confirm what happened in the .log file, where 
the initial temperature is printed.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] velocity generation in Gromacs 2016

[Kukol, Andreas]

Hello,

I always used to generate velocities for an MD run in the equilibation step by 
setting
gen-velyes
in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not 
set. Does it mean velocities are now generated by default ?

http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#mdp

The reason behind my question is, I actually forgot to set it and the 
MD-simulation seemed to run normally.

Many thanks
Andreas
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Re: [gmx-users] Having WCA bonded interaction with FENE potential

[Mark Abraham]

Hi,

Sounds like one approach might be to use FENE bonds, normal exclusions = 3
(or whatever), and to add [ pairs ] function type 1 for each bonded
interaction, and thereby implement your WCA. But these approaches might
differ in how VDW interactions between atoms separated by more than one
bond are computed, and I'm not sure from your description what you intend.
So choose carefully.

Mark

On Tue, Jan 24, 2017 at 3:40 PM ARNAB MUKHERJEE 
wrote:

> Hello,
>
> I am simulating a charged bead-spring modelled polyelectrolyte with FENE
> bond stretching potential and Deby Huckel potential for electrostatics. I
> need to combine FENE bonded interaction combined with WCA potential,
> otherwise the beads overlap with each other since there is no replusive
> term. Before this I ran the same system with no electrostatics, so to take
> into account WCA for bonded interaction I did No. of bonded exclusions
> nexcl = 0, and the results of the simulation seem to be ok.
>
> Now for the same system with electrostatics, if I do nexcl = 0, then there
> will also be electrostatic repulsion between the bonded beads, which I do
> not want. So, how can I have WCA interaction between the bonded atoms,
> without having electrostatic interaction between them?
>
> I know in worst case, I can build a table for the bond stretching
> potential, where I can add the WCA term with FENE potential. But is there
> an easier way to do this? As FENE potential is already there as one of the
> bonded interactions in gromacs.
>
> Thanks a lot,
>
> Regards,
>
> Arnab Mukherjee
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[gmx-users] Having WCA bonded interaction with FENE potential

[ARNAB MUKHERJEE]

Hello,

I am simulating a charged bead-spring modelled polyelectrolyte with FENE
bond stretching potential and Deby Huckel potential for electrostatics. I
need to combine FENE bonded interaction combined with WCA potential,
otherwise the beads overlap with each other since there is no replusive
term. Before this I ran the same system with no electrostatics, so to take
into account WCA for bonded interaction I did No. of bonded exclusions
nexcl = 0, and the results of the simulation seem to be ok.

Now for the same system with electrostatics, if I do nexcl = 0, then there
will also be electrostatic repulsion between the bonded beads, which I do
not want. So, how can I have WCA interaction between the bonded atoms,
without having electrostatic interaction between them?

I know in worst case, I can build a table for the bond stretching
potential, where I can add the WCA term with FENE potential. But is there
an easier way to do this? As FENE potential is already there as one of the
bonded interactions in gromacs.

Thanks a lot,

Regards,

Arnab Mukherjee
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Re: [gmx-users] GPU file

[RAHUL SURESH]

 gmx mdrun -rerun md.xtc deffnm md in my cpu.

Hope this will get me the necessary file. Isnt it?

On Tue, Jan 24, 2017 at 4:10 PM, Mark Abraham 
wrote:

> Hi,
>
> As the md.log file reports, energy groups aren't implemented on GPUs. You
> can use
>
> mdrun -s topol.tpr -rerun traj.trr -nb cpu
>
> to get them for the frames you saved.
>
> Mark
>
> On Tue, Jan 24, 2017 at 10:54 AM RAHUL SURESH 
> wrote:
>
> > Why is that ENERGY is 0 when simulation is from GPU.
> >
> > and how to get the energy file by running in in cpu
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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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> >
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Dihedral Population Analysis -Index file

[Mark Abraham]

Hi,

On Tue, Jan 24, 2017 at 12:35 AM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear Gromacs users,
>
> I have a trajectory file which I wish to do a dihedral analysis for
> specific dihedral.
> Based on what I understood from mailing list and manual, I made an
> index.ndx manually for the dihedral of interest in the molecule.
>
> Usually, when we make an index file, say for atom P in the system, make_ndx
> makes an index file which includes the numbers for all the P atom in the
> system. These numbers are the index numbers in the .gro file for the whole
> system.
>
> In my index file, I made it based on the atom numbers in the topology file
> for the lipid.
>

That forces you to use a trajectory file that contains only a single lipid.
With suitable index groups (for which I recommend gmx select), there's no
need to do that.


> For doing analysis, I first used trjconv and saved only the .xtc file for
> only the lipid of interest, and then used g_angle to calculate the dihedral
> population. I think what I get is only for ONE lipid over time NOT an
> average over time and lipids in the system.
>

Perforce. You only gave gmx angle one lipid and used an index group with
one dihedral. Whether you got a time series, an average or a distribution
depends on what you did with gmx angle.


> The obvious solution would be to include all the dihedrals for all the
> lipids in it.
> BUT, this is not easy to do manually. I tried mk_angndx but it is not
> giving me what I want.
> Is there any way to do this?
>

Sure, see
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

Something along the lines of

resname POPC and name C2 C3 C4 C5

will produce a group that has that dihedral from every POPC.

Mark


> Thanks in advance for any comment and suggestion
>
> Cheers
> Mohsen
>
> --
> *Rewards work better than punishment ...*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] simulation of ternary complex

[Erik Marklund]

Dera Maria,

Yes that is possible. Be sure to make a good choice of forcefield, so that you 
have decent parameters for all molecule types in your simulation.

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 24 Jan 2017, at 11:25, maria khan 
> wrote:

Dear gromacs Users..

I want to simulate ternary complex of protein -DNA -ligand..Is it possible
to simulate it combinely?

secondly..Gromacs has no graphical interface to visualize results..how can
we resolve this issue..Using VMD i have some issues regarding trajectories..

Regards..

Maria khan.

ICS,,university of peshawar..
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Re: [gmx-users] GPU file

[Mark Abraham]

Hi,

As the md.log file reports, energy groups aren't implemented on GPUs. You
can use

mdrun -s topol.tpr -rerun traj.trr -nb cpu

to get them for the frames you saved.

Mark

On Tue, Jan 24, 2017 at 10:54 AM RAHUL SURESH 
wrote:

> Why is that ENERGY is 0 when simulation is from GPU.
>
> and how to get the energy file by running in in cpu
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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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>
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>
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Re: [gmx-users] simulation of ternary complex

[Amir Zeb]

I want to simulate ternary complex of protein -DNA -ligand..Is it possible
to simulate it combinely?

Yeah sure, you can, your order might be protein-DNA-ligand during topology
development and gro file format

good luck

On Tue, Jan 24, 2017 at 2:25 AM, maria khan 
wrote:

> Dear gromacs Users..
>
> I want to simulate ternary complex of protein -DNA -ligand..Is it possible
> to simulate it combinely?
>
> secondly..Gromacs has no graphical interface to visualize results..how can
> we resolve this issue..Using VMD i have some issues regarding
> trajectories..
>
> Regards..
>
> Maria khan.
>
> ICS,,university of peshawar..
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[gmx-users] simulation of ternary complex

[maria khan]

Dear gromacs Users..

I want to simulate ternary complex of protein -DNA -ligand..Is it possible
to simulate it combinely?

secondly..Gromacs has no graphical interface to visualize results..how can
we resolve this issue..Using VMD i have some issues regarding trajectories..

Regards..

Maria khan.

ICS,,university of peshawar..
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[gmx-users] GPU file

[RAHUL SURESH]

Why is that ENERGY is 0 when simulation is from GPU.

and how to get the energy file by running in in cpu

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] How to concatenate tpr files?

[Erik Marklund]

Dear Leila,

The RMSD is, by default, calculated with respect to the coordinates in the tpr 
file, which is why you get different results with different tprs. Which one to 
choose depends on exactly what you want to measure.

Kind regards,
Erik

__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se

On 23 Jan 2017, at 17:10, leila karami 
> wrote:

Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?

Best
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