Re: [gmx-users] Multisite ion of Mg in Gromacs

[Quyen Vu]

Dear all,
Could anyone can please help me clarify the last paragraph on page 393 of
gromacs manual 2019.1?

"when sigma and epsilon need to be supplied (rule 2 and 3), it would seem
it is impossible to have non-zero C12 combined with a zero C6 parameter.
However, providing a negative sigma will do exactly that, such that C6 is
set to zero and C12 is calculated normally"

If the reference uses the potential function: U_{ij}=Aij/r_{ij}^12
-B_{ij}/r_{ij}^6 and provide A_i=0.05, B_i=0, how can I convert to epsilon
and sigma in Gromacs (using amber99sb force field)?
Thank you and best regards,


On Fri, May 24, 2019 at 12:15 PM Quyen Vu  wrote:

> Dear GMX users,
> I want to use multisite ion model for Mg2+ and I follow the parameters set
> of the paper: https://pubs.acs.org/doi/10.1021/jp501737x
> Here they develop these parameters for Q package. In the Lennard-Jones
> potentials, they use Aij, Bij terms (eq. 1) while Gromacs use epsilon and
> sigma term. The dummy atoms in their model have the repulsive term (Ai) but
> not attractive term (Bi=0).
>  How can I remove the attractive term of dummy atoms in Gromacs?
> Best regards,
> Quyen
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 64

[ABEL Stephane]

Hello Azadeh

For the calculations of the EDP you have to take into account of the charges of 
the atom (it is mentioned at the end of density tool ("known issue")) . So 
modify the number of electrons to have the "real" electron numbers in you 
electron.dat file accordingly.

HTH 


--

Message: 1
Date: Sat, 25 May 2019 13:21:32 +0200
From: Azadeh Alavizargar 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Calculating electron density profile of a lipid
bilayer system
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear Gromacs users

I am trying to calculate the electron density profiles of a lipid bilayer
system. However I am not getting the correct profile. I would appreciate it
a lot if you can help me.

Following is the procedure I go through:

1- first I create a ndx file to select the resnames:

gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
'(resname DPPC TIP3)'

2- Then I created the electron.dat file including all the atoms (including
hydrogens) of the selected atoms. The first lines look like this:
208
OH = 8
H1 = 1
H2 = 1
N = 7
C13 = 6
H13A = 1
H13B = 1
H13C = 1
C14 = 6
H14A = 1
H14B = 1
H14C = 1
C15 = 6
...

3- Then I use gmx density in order to calculate the electron density of the
selected resnames:

gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
 density_traj_center.xvg -dens electron -ei electron.dat -center -relative

However,  what I get is not similar to the ones in papers:
Best regards,
Azadeh
[image: image.png]

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Re: [gmx-users] Pressure coupling problem

[Gregory Man Kai Poon]

Hi Ben,

Could you try your simulation on another GROMACS build (on a different machine 
perhaps) to isolate the functional cause of your symptoms?  Or perhaps use 
another FF on the same structure?  I think this would be of interest to many 
users.

Best wishes,

Gregory


On 5/25/2019 5:33 AM, Tam, Benjamin wrote:

Hi Jacob,

Thank you for your responses. My system is set up for generating a polymer with 
over 40800 atoms. So initially, I need to simulate the system in different 
pressure in order to set up a "correct" simulation system. I have simulated 
with Berendsen barostat for 10 ns and through the density and energy plot, I 
can confirm that the system box size has remained stable. Yet with P-R 
barostat, the explosion happened with 100 ps and somehow the system can 
continue to run. There is no restraint or constraint to the atom or to the box. 
I even check it with a box filled with  TIP4P water molecules alone, the box 
still exploded with P-R.

However, when I changed the version. It seems like the problem are solved, 
which is rather strange and unbelievable.

Best,

Ben

From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 

 on behalf of Jacob Monroe 

Sent: 24 May 2019 18:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure coupling problem

Hi Ben,

I haven’t seen a response yet, so since I’ve encountered this type of thing 
before, I’ll chime in with my two cents.

I’ve run into similar issues before, and it’s always turned out to be something 
with the way I set up the simulation.  What I’ve found is that if things tend 
to explode with the Parinello-Rahman barostat, they are also exploding with the 
Berendsen barostat, just at a slower rate due to the tendency of the latter 
algorithm to incorrectly over dampen fluctuations.  I’ve also found that some 
simulations stay stable for longer than others simply by chance, but if you run 
long enough, they will eventually explode as well.  My recommendation is to 
watch the simulation box carefully or plot its dimension over time - if it just 
keeps growing, now matter how slowly, you have a problem.

Do you have any atoms in the box frozen?  Or position restraints with large 
spring constants?  Sometimes restraints for holding two molecules close to each 
other, depending on the system, can also cause odd behavior.  Without knowing 
more about your system, I’ll also ask, do you actually need a barostat, or will 
NVT be fine?  Or are there ways to relax your system to an appropriate density 
without seeing the problem behavior?

Best,
Jacob

On May 23, 2019, at 10:23 AM, Tam, Benjamin 
mailto:benjamin.tam...@ucl.ac.uk>>
 wrote:

Dear all,

To follow through with this email. It seems like the barostat problem comes 
from a different version. As I tested with version 
gromacs/2016.3/intel-2017-update1, the system remains stable for 1 ns and the 
same system explode with gromacs/2018.3/intel-2018.

Was there some kind of bug in the newer version or am I missing something?

Best,

Ben
-Original Message-
From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 
mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>>
 On Behalf Of Tam, Benjamin
Sent: 23 May 2019 11:40
To: 
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Pressure coupling problem

Dear Gromacs user,

Currently, I am baffled about a simulation that I am running and I hope I will 
find some answer here.

Initially, I have run my system with Berendsen barostat to equilibrate for 1 
ns. The system looks fine as there is no box explosion.

However, after the equilibration, I change the barostat to Parinello-Rahman. 
The box exploded. I tried to debug my system by turning off Lennard Jones and 
charge (separately and together). Yet the box still explodes without any 
reason. The system is set as 300K and 1 bar.

Here, I have to mention that the intramolecular bond is correct as the 
molecules did not explode. The only difference is the barostat that I have 
varied. Therefore, can anyone give me some clue what is going and why changing 
the barostat will cause this effect?

Thank you very much.

Best regards,

Ben
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Re: [gmx-users] RMSD for specified length of DNA aptamer

[Quyen Vu]

Hi,
You should create an index file (use gmx make_ndx) that contains a list of
the atom you want to perform RMSD calculation on, e.g P atoms, or whatever
you want.
Then when you run gmx rms, you have to pass the index file from the above
step
Best,

On Sat, May 25, 2019 at 11:41 AM mmousivand93  wrote:

> Dear all
>
> I have been run molecular dynamic simulation between DNA(50bp)and small
> ligand,how to calculate RMSD value for
>
> specified length of DNA during 50ns simulation(for example  residues
> from 12 to 25)?
>
> Best Regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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[gmx-users] Calculating electron density profile of a lipid bilayer system

[Azadeh Alavizargar]

Dear Gromacs users

I am trying to calculate the electron density profiles of a lipid bilayer
system. However I am not getting the correct profile. I would appreciate it
a lot if you can help me.

Following is the procedure I go through:

1- first I create a ndx file to select the resnames:

gmx select -f trj_file.trr -s tpr_file.tpr -on index_file.ndx -select
'(resname DPPC TIP3)'

2- Then I created the electron.dat file including all the atoms (including
hydrogens) of the selected atoms. The first lines look like this:
208
OH = 8
H1 = 1
H2 = 1
N = 7
C13 = 6
H13A = 1
H13B = 1
H13C = 1
C14 = 6
H14A = 1
H14B = 1
H14C = 1
C15 = 6
...

3- Then I use gmx density in order to calculate the electron density of the
selected resnames:

gmx density -f trj_file.trr -s tpr_file.tpr -n index_file.ndx -o
 density_traj_center.xvg -dens electron -ei electron.dat -center -relative

However,  what I get is not similar to the ones in papers:
Best regards,
Azadeh
[image: image.png]
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[gmx-users] Use of index file generated by gmx select

[Soham Sarkar]

Hello,
I have a 500ns trajectory of protein-water-urea mixture, saved at 2ps
interval. I am using gmx select to generate a index.ndx of 25 index for
water molecules within 0.5nm of the protein. I want to know how to use this
index.ndx file for my calculation -
For example:
a) If I want to calculate the velocity autocorrelation using gmx velacc of
those water molecules within 0.5nm of the protein.
b) The orientation of those  water molecules using the dipole of water
using gmx h2order
c) The tetrahedral order parameter for those particular water molecules
how should I use the index file? Please provide me with the command and the
process of calculation.
Thanks and regards-
Soham
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[gmx-users] RMSD for specified length of DNA aptamer

[mmousivand93]

Dear all 

I have been run molecular dynamic simulation between DNA(50bp)and small
ligand,how to calculate RMSD value for 

specified length of DNA during 50ns simulation(for example  residues
from 12 to 25)?

Best Regards
-- 
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Re: [gmx-users] Pressure coupling problem

[Tam, Benjamin]

Hi Jacob,

Thank you for your responses. My system is set up for generating a polymer with 
over 40800 atoms. So initially, I need to simulate the system in different 
pressure in order to set up a "correct" simulation system. I have simulated 
with Berendsen barostat for 10 ns and through the density and energy plot, I 
can confirm that the system box size has remained stable. Yet with P-R 
barostat, the explosion happened with 100 ps and somehow the system can 
continue to run. There is no restraint or constraint to the atom or to the box. 
I even check it with a box filled with  TIP4P water molecules alone, the box 
still exploded with P-R.

However, when I changed the version. It seems like the problem are solved, 
which is rather strange and unbelievable.

Best,

Ben

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jacob Monroe 

Sent: 24 May 2019 18:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure coupling problem

Hi Ben,

I haven’t seen a response yet, so since I’ve encountered this type of thing 
before, I’ll chime in with my two cents.

I’ve run into similar issues before, and it’s always turned out to be something 
with the way I set up the simulation.  What I’ve found is that if things tend 
to explode with the Parinello-Rahman barostat, they are also exploding with the 
Berendsen barostat, just at a slower rate due to the tendency of the latter 
algorithm to incorrectly over dampen fluctuations.  I’ve also found that some 
simulations stay stable for longer than others simply by chance, but if you run 
long enough, they will eventually explode as well.  My recommendation is to 
watch the simulation box carefully or plot its dimension over time - if it just 
keeps growing, now matter how slowly, you have a problem.

Do you have any atoms in the box frozen?  Or position restraints with large 
spring constants?  Sometimes restraints for holding two molecules close to each 
other, depending on the system, can also cause odd behavior.  Without knowing 
more about your system, I’ll also ask, do you actually need a barostat, or will 
NVT be fine?  Or are there ways to relax your system to an appropriate density 
without seeing the problem behavior?

Best,
Jacob

On May 23, 2019, at 10:23 AM, Tam, Benjamin 
mailto:benjamin.tam...@ucl.ac.uk>> wrote:

Dear all,

To follow through with this email. It seems like the barostat problem comes 
from a different version. As I tested with version 
gromacs/2016.3/intel-2017-update1, the system remains stable for 1 ns and the 
same system explode with gromacs/2018.3/intel-2018.

Was there some kind of bug in the newer version or am I missing something?

Best,

Ben
-Original Message-
From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 
mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>>
 On Behalf Of Tam, Benjamin
Sent: 23 May 2019 11:40
To: 
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Pressure coupling problem

Dear Gromacs user,

Currently, I am baffled about a simulation that I am running and I hope I will 
find some answer here.

Initially, I have run my system with Berendsen barostat to equilibrate for 1 
ns. The system looks fine as there is no box explosion.

However, after the equilibration, I change the barostat to Parinello-Rahman. 
The box exploded. I tried to debug my system by turning off Lennard Jones and 
charge (separately and together). Yet the box still explodes without any 
reason. The system is set as 300K and 1 bar.

Here, I have to mention that the intramolecular bond is correct as the 
molecules did not explode. The only difference is the barostat that I have 
varied. Therefore, can anyone give me some clue what is going and why changing 
the barostat will cause this effect?

Thank you very much.

Best regards,

Ben
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