Re: [gmx-users] Free Energy calculation

[Anjali Patel]

Hello,

Thank you for the quick reply @ Mark Abraham. I am describing in detail
what i want to do. I have taken SWCNT (12*12)and encapsulate the molecule.
Now i want to check its binding free energy. I checked reference manual to
arrange the right order but didn’t success. can anyone have any other link
or example file. I am stuck over here. please help to solve this.


With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002
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Re: [gmx-users] GPU Command

[Nikhil Maroli]

Refer this
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html

I use  -ntmpi and  -ntomp combination with -gpu_id
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Re: [gmx-users] calculating pairwise interactions

[Nikhil Maroli]

Changing these parameters is not good, you may need to refer the forcefield
original articles.
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Re: [gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

[Mark Abraham]

Hi,

Make sure your particles have vdw on before you add charge to them. That's
usually the cause of this problem.

Mark

On Mon, Apr 16, 2018, 20:51 faride badalkhani 
wrote:

>  Dear all,
> I am trying to perform free energy calculations of a small drug in octanol
> using the GROMACS 5.1.3 software. I built a box of octanol using the
> following command
> gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro
> Followed by steepest descent minimization, 100 ps each of NVT
> and NPT equilibration and 10 ns of production MD. Then, I centered the drug
> into the equilibrated box using editconf and performed a same procedure as
> the octanol bax to equilibrate the drug-octanol system. All minimization,
> equilibration and production simiulations were done without any error and
> the plots showd that the system had been equilibrated well. Finally, I
> performed the free energy calculations but at MD step I got the following
> error:
> WARNING: Listed nonbonded interaction between particles X and Y at distance
> 2.2 which is larger than the table limit 2.2 nm.
> > > This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed, they
> are skipped until they are inside the table limit again. You will only see
> this message once, even if it occurs for several interactions.
> > > IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
> Could you help me with this problem, please?
> Best.
> Farideh
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[gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

[faride badalkhani]

 Dear all,
I am trying to perform free energy calculations of a small drug in octanol
using the GROMACS 5.1.3 software. I built a box of octanol using the
following command
gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro
Followed by steepest descent minimization, 100 ps each of NVT
and NPT equilibration and 10 ns of production MD. Then, I centered the drug
into the equilibrated box using editconf and performed a same procedure as
the octanol bax to equilibrate the drug-octanol system. All minimization,
equilibration and production simiulations were done without any error and
the plots showd that the system had been equilibrated well. Finally, I
performed the free energy calculations but at MD step I got the following
error:
WARNING: Listed nonbonded interaction between particles X and Y at distance
2.2 which is larger than the table limit 2.2 nm.
> > This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed, they
are skipped until they are inside the table limit again. You will only see
this message once, even if it occurs for several interactions.
> > IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
Could you help me with this problem, please?
Best.
Farideh
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Re: [gmx-users] Definiting protonation in pdb2gmx input

[mhuhtala]

Quoting Justin Lemkul :

problem. Please file a bug report on Redmine and include example input
files and pdb2gmx syntax you're using.


Ok, thanks. Bug posted at https://redmine.gromacs.org/issues/2480



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Re: [gmx-users] Definiting protonation in pdb2gmx input

[Justin Lemkul]

On 4/16/18 9:44 AM, mhuht...@abo.fi wrote:

Quoting Justin Lemkul :


I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?


Is this behavior documented somewhere? I don't seem to find any 
mention of it.


It's always been default behavior - if pdb2gmx matches a residue name, 
it processes the coordinates according to the .rtp file.




My initial problem was that when I attempted to use a structure with 
hydrogens (polar only) as input, I just got a lot of error messages 
about atom names and the numbers of atoms not matching the residue 
topology, which made me assume that pdb2gmx simply does not do the trick.




As you mention below, you're using a UA force field, which won't have 
most of the H atoms you are supplying, so you'll get errors. Using -ignh 
should fix that (but then again, see below).


Now I did a bit more testing, and at least renaming ASP to ASPH in the 
input will get me an ASPH in the output, but only the residue name, 
not the hydrogen. So I get a residue named ASPH, but the structure is 
an unprotonated ASP. Is this a bug? Or is pdb2gmx expecting to find 
the hydrogen atom line in the input?




All necessary hydrogens should be reconstructed according to the .hdb 
file (for which entries for protonated amino acids exist and are 
functional).


Then I tried changing a HIS to HISA, and that one works. By default, 
pdb2gmx adds two hydrogens to that histidine, but with HISA specified, 
I do get only the hydrogen on ND, as expected.


This is all using Gromacs 2018 and specifying GROMOS96 54a7, and 
modifying a crystal structure PDB file taken from the PDB, with no 
hydrogens.





There does appear to be a problem specifically with united-atom force 
fields. Both CHARMM and AMBER function correctly, with or without -ignh. 
Using any GROMOS variant, with or without -ignh leads to a problem. 
Please file a bug report on Redmine and include example input files and 
pdb2gmx syntax you're using.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Definiting protonation in pdb2gmx input

[mhuhtala]

Quoting Justin Lemkul :


I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?


Is this behavior documented somewhere? I don't seem to find any mention of it.

My initial problem was that when I attempted to use a structure with  
hydrogens (polar only) as input, I just got a lot of error messages  
about atom names and the numbers of atoms not matching the residue  
topology, which made me assume that pdb2gmx simply does not do the  
trick.


Now I did a bit more testing, and at least renaming ASP to ASPH in the  
input will get me an ASPH in the output, but only the residue name,  
not the hydrogen. So I get a residue named ASPH, but the structure is  
an unprotonated ASP. Is this a bug? Or is pdb2gmx expecting to find  
the hydrogen atom line in the input?


Then I tried changing a HIS to HISA, and that one works. By default,  
pdb2gmx adds two hydrogens to that histidine, but with HISA specified,  
I do get only the hydrogen on ND, as expected.


This is all using Gromacs 2018 and specifying GROMOS96 54a7, and  
modifying a crystal structure PDB file taken from the PDB, with no  
hydrogens.





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Re: [gmx-users] gromos54a7 - topolbuild

[Ray, Bruce D]

On Apr 16, 2018, at 7:57 AM,  wrote:

> Date: Mon, 16 Apr 2018 06:28:52 -0400
> From: Alex 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] gromos54a7 - topolbuild
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
> 
> Dear all,
> I wonder if the topolbuild can provide the gromos 54A7 (gmx54a7) FF?
> 
> Regards,
> Alex


The standard files for topolbuild do not contain anything for gmx54a7.  Since 
these
are text files, it should be simple to follow the examples of the gmx files 
given
and build equivalent files for gmx54a7 given appropriate data from gmx54a7.
However this has not been done.  Alternatively, it should be simple to use one
of the gmx files given in topolbuild to generate the outline, and to edit the
topolbuild output with a text editor as needed to use gmx54a7 parameters.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


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Re: [gmx-users] Gmx_solvate

[Justin Lemkul]

On 4/16/18 8:51 AM, rose rahmani wrote:

Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?


Yes.


So trjorder can fix the rest, yes?


No, but trjconv can save what you want based on an index group from gmx 
select.


-Justin


On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:



On 4/16/18 5:58 AM, rose rahmani wrote:

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8

to

12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to

start

from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it

in

a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific

dimensions?

No.


Would you please help me?

Write a script to remove solvent molecules based on coordinates, or use
gmx select write an index group to do the same.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Gmx_solvate

[rose rahmani]

Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?
So trjorder can fix the rest, yes?

On Mon, 16 Apr 2018, 16:26 Justin Lemkul,  wrote:

>
>
> On 4/16/18 5:58 AM, rose rahmani wrote:
> > Hi,
> >
> > I have input structure from my last simulation. The box is 12nm long in Z
> > axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8
> to
> > 12 is empty) .  I want to add solvent between z=3-8. How can i do that?
> > The problem is that i cant adjust wall and sheet( z coordination) to
> start
> > from z=0 of box.
> > I mean when i extract wall and sheet from my last simulation and open it
> in
> > a viewer they wont start from 0, which is not odd. So i cant use the box
> > size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
> > larger.
> > What is your idea? Is there any tool to add solvate in specific
> dimensions?
>
> No.
>
> > Would you please help me?
>
> Write a script to remove solvent molecules based on coordinates, or use
> gmx select write an index group to do the same.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] build virus envelop

[Justin Lemkul]

On 4/15/18 9:22 PM, sunyeping wrote:

Dear everyone,

Do you have a tutorial of building a virus lip bilayer envelope with its 
glycoproteins for MD simulation? Recenetly some MD simulation have done with 
the envelope  of some viruses such as influenza virus (Reddy et al., 2015) and 
dengue virus (Marzinek et al., 2016, Structure). However, I cannot find a 
detailed description about the envelope building model process. I would whether 
anyone here has an expertise of doing this and could give me some guidance.


Have you tried contacting the corresponding authors of those papers? 
That's why they're listed.


-Justin

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Dihedral Angle Distribution

[Justin Lemkul]

On 4/16/18 3:07 AM, Anjana Jayasinghe wrote:

Dear Gromacs Users,
I want to calculate dihedral angle distribution for 9 dihedral angles in 
aliphatic chain of my molecule. I created the index file giving the command 
make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14 a 
C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a C17 a C18 a C19a C17 a C18 a C19 
a C20a C18 a C19 a C20 a C21a C19 a C20 a C21 a C22a C20 a C21 a C22 a C23a C21 
a C22 a C23 a C24
When I checked the index file, all cerated groups contains more than four 
columns as below. I would like to know, is this correct or wrong? Since we need 
4 atoms to represent the dihedral angle, [ C13_A_C14_A_C15_A_C16 ] group should 
contain 4 columns as highlighted below? I'm bit confused. Appreciate if anyone 
help me.
[ C13_A_C14_A_C15_A_C16 ]
   21   22   23   24   53   54   55   56   85   86   87   88  117  118  119
  120  149  150  151  152  181  182  183  184  213  214  215  216  245  246
  247  248  277  278  279  280  309  310  311  312  341  342  343  344  373
  374  375  376  405  406  407  408  437  438  439  440  469  470  471  472
  501  502  503  504  533  534  535  536  565  566  567  568  597  598  599
  600  629  630  631  632  661  662  663  664  693  694  695  696  725  726
  
The other thing I want to know is, when I tried to calculate, angle 
distribution using the gromacs command,
g_angle -f *.xtc -of Dihed.xvg -b 99000 -e 10 -n dihedral.ndx -type 
dihedral, I got xvg file name as angdist.xvg instead of Dihed.xvg.


Because you didn't ask for a file named "Dihed.xvg" - the default output 
file name for the -od option is "angdist.xvg" so that's what g_angle wrote.


The index file is fine, when you specify dihedral mode, the program 
reads in groups of four numbers.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Definiting protonation in pdb2gmx input

[Justin Lemkul]

On 4/16/18 7:07 AM, mhuht...@abo.fi wrote:


One of the recurring questions on the list seems to be how to define 
residue protonation states non-interactively in pdb2gmx input. The 
interactive options are a bit of a nightmare to use. Could pdb2gmx be 
modified to optionally read the residue types from the PDB file 
itself? The user would replace e.g. "ASP " with "ASPH" in the PDB 
file, and pdb2gmx would build a protonated aspartate, whether the 
hydrogen atom is there in the PDB file or not. Same for all residue 
types, of course. The upside would be having readable and more easily 
scriptable input instead of trying to script the interactive input. I 
realize that the names of the residue types differ between force 
fields, but even requiring force field specific names would be ok as 
far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.).





I just tested this in GROMACS 2018 and it works fine - if you provide 
the protonated residue name, pdb2gmx correctly interprets the 
protonation state. Do you have a use case that fails?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Gmx_solvate

[Justin Lemkul]

On 4/16/18 5:58 AM, rose rahmani wrote:

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to start
from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it in
a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific dimensions?


No.


Would you please help me?


Write a script to remove solvent molecules based on coordinates, or use 
gmx select write an index group to do the same.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Definiting protonation in pdb2gmx input

[mhuhtala]

One of the recurring questions on the list seems to be how to define  
residue protonation states non-interactively in pdb2gmx input. The  
interactive options are a bit of a nightmare to use. Could pdb2gmx be  
modified to optionally read the residue types from the PDB file  
itself? The user would replace e.g. "ASP " with "ASPH" in the PDB  
file, and pdb2gmx would build a protonated aspartate, whether the  
hydrogen atom is there in the PDB file or not. Same for all residue  
types, of course. The upside would be having readable and more easily  
scriptable input instead of trying to script the interactive input. I  
realize that the names of the residue types differ between force  
fields, but even requiring force field specific names would be ok as  
far as I'm concerned (ASPH in Gromos, ASH in Amber, etc.).



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[gmx-users] gromos54a7 - topolbuild

[Alex]

Dear all,
I wonder if the topolbuild can provide the gromos 54A7 (gmx54a7) FF?

Regards,
Alex
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[gmx-users] Gmx_solvate

[rose rahmani]

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to start
from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it in
a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific dimensions?
Would you please help me?

Best regards
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[gmx-users] REMD Simulation

[ISHRAT JAHAN]

Dear all,
I am trying to do REMD simulation in different cosolvents. I have generated
temperatures using temperature genrating tools but it gives different
number of temperatures in different solvents with exchange probability of
0.25. Is it fair to do remd with different replicas? In what way it will
effect the results?
Thankyou
-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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[gmx-users] Dihedral Angle Distribution

[Anjana Jayasinghe]

Dear Gromacs Users,
I want to calculate dihedral angle distribution for 9 dihedral angles in 
aliphatic chain of my molecule. I created the index file giving the command 
make_ndx -f run.gro -o dihedral.ndxThen  I typed,a C13 a C14 a C15 a C16a C14 a 
C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a C17 a C18 a C19a C17 a C18 a C19 
a C20a C18 a C19 a C20 a C21a C19 a C20 a C21 a C22a C20 a C21 a C22 a C23a C21 
a C22 a C23 a C24
When I checked the index file, all cerated groups contains more than four 
columns as below. I would like to know, is this correct or wrong? Since we need 
4 atoms to represent the dihedral angle, [ C13_A_C14_A_C15_A_C16 ] group should 
contain 4 columns as highlighted below? I'm bit confused. Appreciate if anyone 
help me.
[ C13_A_C14_A_C15_A_C16 ]
  21   22   23   24   53   54   55   56   85   86   87   88  117  118  119
 120  149  150  151  152  181  182  183  184  213  214  215  216  245  246
 247  248  277  278  279  280  309  310  311  312  341  342  343  344  373
 374  375  376  405  406  407  408  437  438  439  440  469  470  471  472
 501  502  503  504  533  534  535  536  565  566  567  568  597  598  599
 600  629  630  631  632  661  662  663  664  693  694  695  696  725  726
 
The other thing I want to know is, when I tried to calculate, angle 
distribution using the gromacs command, 
g_angle -f *.xtc -of Dihed.xvg -b 99000 -e 10 -n dihedral.ndx -type 
dihedral, I got xvg file name as angdist.xvg instead of Dihed.xvg. 

Appreciate, if anyone could help me.
Thank you.






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