Re: [gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

Yes, the system has periodic molecules (periodic-molecules = yes) and the
version of gromacs is 5.1.2. So, I should use for calculating the
properties of the system by gromacs 2016 and newer ones?

Respectfully,
Iman

On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi  wrote:

> Dear Gromacs users,
>
> In using some commands in gromacs, the sentence "There were 240
> inconsistent shifts. Check your topology" come up on the screen and I don't
> know what is wrong in my topology file, however it calculates correctly the
> features of the system but I would like to know the reason of this warning.
>
> Respectfully,
> Iman
>
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Re: [gmx-users] How to obtain TIP4P/ε water model topology file

[Tushar Ranjan Moharana]

Hi Mark,
Thanks a lot for the suggestion. Just need a little more help. As per your
suggestion I should edit the TIP3P topology. But the the forcefield
(CHARMM36) has TIP4P.itp. Is there any advantage to edit  TIP3P.itp instead
of TIP4P.itp. Also I don't know what to edit. According to the concerned
paper, following are the parameter for different  water models. I want the
last water model ( TIP4P/epsilon). But I couldn't find the values mentioned
for the first one when I opened the TIP4P.itp (or TIP3P.itp).

Table 1. Force Field Parameters of Non-Polarizable Water Models
modelσ (Å)epsilon/*k*B (K)*q*H (e)*q*O (e)*l*OM (Å)μ (D)
TIP4P 3.154 78 0.520 0.0 0.15 2.177
TIP4P/2005 3.1589 93.2 0.5564 0.0 0.1546 2.305
TIP4Q 3.1666 93.2 0.525 0.5 0.069 2.44
TIP4P/epsilon 3.165 93.0 0.527 0.0 0.105 2.4345  It will be a great help if
you can help me in modifying the same. Any tutorial or document will be
absolutely fine. Following is how my TIP4P.itp looks like


;
; Note the strange order of atoms to make it faster in gromacs.
;
[ moleculetype ]
; molnamenrexcl
SOL2

[ atoms ]
; idat type res nrresidu name at name cg nrcharge
1   OWT4   1   SOLOW   1   0.0
2   HWT4   1   SOL   HW1   1   0.52
3   HWT4   1   SOL   HW2   1   0.52
4   MWT4   1   SOLMW   1  -1.04

#ifndef FLEXIBLE
[ settles ]
; OWfunctdoh   dhh
110.095720.15139
#else
[ bonds ]
; i jfunctlengthforce.c.
1210.09572 502416.0 0.09572502416.0
1310.09572 502416.0 0.09572502416.0

[ angles ]
; i jkfunctangleforce.c.
2131104.52628.02104.52628.02
#endif

[ exclusions ]
1234
2134
3124
4123

; The position of the virtual site is computed as follows:
;
;O
;
;D
;
;HH
;
; const = distance (OD) / [ cos (angle(DOH))* distance (OH) ]
;  0.015 nm/ [ cos (52.26 deg) * 0.09572 nm]

; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ virtual_sites3 ]
; Vsite fromfunctab
412310.128012065 0.128012065

Thanks a lot.

On Wed, Feb 21, 2018 at 10:48 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi Henriques,
> Thanks a lot for the suggestion. Actually it was TIP4P/(epsilon) which get
> modified to TIP4P/?. I regret for the same. I completely agree with your
> suggestion. Actually in an article (A fully atomistic computer simulation
> study of cold denaturation of a β-hairpin) authors have shown that this
> water model with CHARMM36 forcefield showed the best correlation with the
> experiment. I went through the concern paper where the TIP4P/(epsilon)
> model was tested (Non-Polarizable Force Field of Water Based on the
> Dielectric Constant: TIP4P/ε). However I couldn't get the topology
> (although parameters are mentioned). I have experimental data to verify if
> the water model is not appropriate. It will be a great help if you can help
> me getting/creating the topology.
>
> Thanks a lot for your suggestion.
>
> On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana <
> tusharranjanmohar...@gmail.com> wrote:
>
>> Hi All,
>> I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone
>> let me know where can I get the corresponding .itp file.
>>
>> Thanks a lot.
>>
>> "A society with free knowledge is better than a society with free food"
>> --
>> Tushar Ranjan Moharana
>> B. Tech, NIT Warangal
>> Ph D Student, CCMB
>>
>
>
>
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>



-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] How to obtain TIP4P/ε water model topology file

[Mark Abraham]

Hi,

Make a copy of your force field folder and edit the tip3p.itp file to suit.
Even if someone had done this for you, you'd still want to be able to
verify that this was the only change.

Mark

On Wed, Feb 21, 2018, 06:18 Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi Henriques,
> Thanks a lot for the suggestion. Actually it was TIP4P/(epsilon) which get
> modified to TIP4P/?. I regret for the same. I completely agree with your
> suggestion. Actually in an article (A fully atomistic computer simulation
> study of cold denaturation of a β-hairpin) authors have shown that this
> water model with CHARMM36 forcefield showed the best correlation with the
> experiment. I went through the concern paper where the TIP4P/(epsilon)
> model was tested (Non-Polarizable Force Field of Water Based on the
> Dielectric Constant: TIP4P/ε). However I couldn't get the topology
> (although parameters are mentioned). I have experimental data to verify if
> the water model is not appropriate. It will be a great help if you can help
> me getting/creating the topology.
>
> Thanks a lot for your suggestion.
>
> On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana <
> tusharranjanmohar...@gmail.com> wrote:
>
> > Hi All,
> > I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone
> > let me know where can I get the corresponding .itp file.
> >
> > Thanks a lot.
> >
> > "A society with free knowledge is better than a society with free food"
> > --
> > Tushar Ranjan Moharana
> > B. Tech, NIT Warangal
> > Ph D Student, CCMB
> >
>
>
>
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Thank you
I'm trying to update it for external magnetic filed applications

On Sun, Feb 18, 2018 at 12:57 PM, Mark Abraham 
wrote:

> Hi,
>
> Suggestion, get the git version of gromacs and use
>
>  git grep -i -G"electric field"
>
> src/gromacs/applied-forces
>
> Mark
>
> On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed  wrote:
>
> > Dear Mark,
> > I could not find the electric field calculation code. In 2016 version,
> the
> > code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
> > Is it elsewhere? can you tell me, please?
> > Thanks
> >
> > On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:
> >
> > > Dear Mark,
> > > Thank you. this is good I will study it.
> > >
> > >
> > > On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> See section 6.7 of the 2018 reference manual for what is supported.
> > >>
> > >> MArk
> > >>
> > >> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed 
> wrote:
> > >>
> > >> > Hello GROMACS users
> > >> > I have looked through GROMACS user manual to understand the theory
> > >> behind
> > >> > applying external electric field but I did not find any description.
> > >> Also,
> > >> > I looked at the source code in  sim_util.cpp file but found only the
> > >> > time-dependent electric field.
> > >> > My question does GROMACS consider Lorentz force for applying
> external
> > >> > electric field or using another theory?
> > >> > Thanks
> > >> > Ali
> > >> > --
> > >> > 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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Re: [gmx-users] How to obtain TIP4P/ε water model topology file

[Tushar Ranjan Moharana]

Hi Henriques,
Thanks a lot for the suggestion. Actually it was TIP4P/(epsilon) which get
modified to TIP4P/?. I regret for the same. I completely agree with your
suggestion. Actually in an article (A fully atomistic computer simulation
study of cold denaturation of a β-hairpin) authors have shown that this
water model with CHARMM36 forcefield showed the best correlation with the
experiment. I went through the concern paper where the TIP4P/(epsilon)
model was tested (Non-Polarizable Force Field of Water Based on the
Dielectric Constant: TIP4P/ε). However I couldn't get the topology
(although parameters are mentioned). I have experimental data to verify if
the water model is not appropriate. It will be a great help if you can help
me getting/creating the topology.

Thanks a lot for your suggestion.

On Tue, Feb 20, 2018 at 10:00 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi All,
> I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone
> let me know where can I get the corresponding .itp file.
>
> Thanks a lot.
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>



-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] Calculate RDF within a certain distance from atom

[Dilip H N]

I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm. So, i am further interested in studying how water molecules
are oriented towards it closely...what is happening around within 0.7nm
distance of Calpha w.r.t Ow...

Any suggestions...??

Thank you.




‌
 Sent with Mailtrack


On Tue, Feb 20, 2018 at 10:58 PM, Justin Lemkul  wrote:

>
>
> On 2/20/18 11:53 AM, Dilip H N wrote:
>
>> Hello,
>> How to get RDF within a certain distance..??
>>
>> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
>> atoms within 0.7nm of C-alpha (Calpha-Ow).
>>
>> how can i get it from in-house gmx rdf command...??
>>
>
> What do you hope to achieve from such a metric? RDF has to be normalized
> against bulk occupancy, which will of course not be achieved at a 0.7-nm
> distance. If you are interested in certain properties within given
> solvation shells, distances, etc. compute the normal RDF so that it is
> properly normalized and interpret the outcome of that calculation.
>
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] PROBLEM IN COORDINATES

[Justin Lemkul]

On 2/20/18 9:50 PM, neelam wafa wrote:

Dear gmx users

I am still stuck at this point.
error obtained is this
Fatal error:
number of coordinates in coordinate file (solv.gro, 32803)
  does not match topology (topol.top, 32818)
There is a difference of 15. I think its not considering the ligand as 15
is i think for ligand. the ligand. the entries of ligand in gro file are
these.
15
 1JZ4  C4   1   2.946  -2.601   0.141
 1JZ4  C14  2   3.009  -2.568   0.005
 1JZ4  C13  3   2.965  -2.664  -0.107
 1JZ4  C12  4   2.834  -2.642  -0.154
 1JZ4  C11  5   2.734  -2.734  -0.116
 1JZ4  H11  6   2.753  -2.810  -0.040
 1JZ4  C7   7   2.606  -2.727  -0.176
 1JZ4  H7   8   2.529  -2.798  -0.147
 1JZ4  C8   9   2.578  -2.628  -0.273
 1JZ4  H8  10   2.479  -2.624  -0.319
 1JZ4  C9  11   2.677  -2.536  -0.311
 1JZ4  H9  12   2.655  -2.460  -0.387
 1JZ4  C10 13   2.804  -2.543  -0.251
 1JZ4  OAB 14   2.900  -2.451  -0.285
 1JZ4  HAB 15   2.863  -2.389  -0.354
0.68000   0.68000   0.68000

Help me out please.


Looks like you probably didn't copy the ligand coordinates into the 
topology. The topology thinks it's there and the coordinates say it's 
not. The solution to this error is always the same: proper bookkeeping.


-Justin

--
==

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

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

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Re: [gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

Dear gmx users

I am still stuck at this point.
error obtained is this
Fatal error:
number of coordinates in coordinate file (solv.gro, 32803)
 does not match topology (topol.top, 32818)
There is a difference of 15. I think its not considering the ligand as 15
is i think for ligand. the ligand. the entries of ligand in gro file are
these.
15
1JZ4  C4   1   2.946  -2.601   0.141
1JZ4  C14  2   3.009  -2.568   0.005
1JZ4  C13  3   2.965  -2.664  -0.107
1JZ4  C12  4   2.834  -2.642  -0.154
1JZ4  C11  5   2.734  -2.734  -0.116
1JZ4  H11  6   2.753  -2.810  -0.040
1JZ4  C7   7   2.606  -2.727  -0.176
1JZ4  H7   8   2.529  -2.798  -0.147
1JZ4  C8   9   2.578  -2.628  -0.273
1JZ4  H8  10   2.479  -2.624  -0.319
1JZ4  C9  11   2.677  -2.536  -0.311
1JZ4  H9  12   2.655  -2.460  -0.387
1JZ4  C10 13   2.804  -2.543  -0.251
1JZ4  OAB 14   2.900  -2.451  -0.285
1JZ4  HAB 15   2.863  -2.389  -0.354
   0.68000   0.68000   0.68000

Help me out please.

Regards

On Sun, Feb 18, 2018 at 6:45 PM, Alex  wrote:

> Hi,
>
> The error is informative. Check the number of entries in the gro file and
> compare it with the [ atoms ] section in your topology, together with
> anything that's added under [ system ]. The total numbers need to match.
>
> Alex
>
>
>
> On 2/18/2018 11:34 AM, neelam wafa wrote:
>
>> Dear gmx users,
>>
>> I am doing the tutorial of protein ligand simmulation given at
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/com.
>> when I give following command, I get an error.
>>
>> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>
>> the error says the number of coordinates in the sol.gro file and
>> topol.top file does not match. How to fix it.
>>
>> Help me out please.
>>
>> Thanks in advance.
>>
>> Regards
>>
>
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Re: [gmx-users] About rdf in membranes

[Justin Lemkul]

On 2/20/18 7:42 PM, Poncho Arvayo Zatarain wrote:

The -xy is after or before the .ndx. I have this command gmx rdf -f file.xtc -s 
file.tpr -n file.ndx -xy -o file.xvg


It doesn't matter. It's a boolean flag so it can appear anywhere in the 
command line that doesn't disrupt any other argument/filename pair.


-Justin




De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: martes, 20 de febrero de 2018 04:33 p. m.
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] About rdf in membranes



On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote:

Hello Gromacs Users: I want to calculate rdf in membranes. I read i need 
something like .xy and i´m a little confussed. The command will be: gmx rdf -f 
file.xtc -s file.tpr -n file.ndx -xy -o file.xvg=

What point is confusing?

-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
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Justin Lemkul
www.biochem.vt.edu




==

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

303 Engel Hall
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Re: [gmx-users] About rdf in membranes

[Poncho Arvayo Zatarain]

The -xy is after or before the .ndx. I have this command gmx rdf -f file.xtc -s 
file.tpr -n file.ndx -xy -o file.xvg



De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: martes, 20 de febrero de 2018 04:33 p. m.
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] About rdf in membranes



On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote:
>
> Hello Gromacs Users: I want to calculate rdf in membranes. I read i need 
> something like .xy and i´m a little confussed. The command will be: gmx rdf 
> -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg=

What point is confusing?

-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.biochem.vt.edu/people/faculty/JustinLemkul.html
Justin Lemkul
www.biochem.vt.edu




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Re: [gmx-users] About rdf in membranes

[Justin Lemkul]

On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote:


Hello Gromacs Users: I want to calculate rdf in membranes. I read i need 
something like .xy and i´m a little confussed. The command will be: gmx rdf -f 
file.xtc -s file.tpr -n file.ndx -xy -o file.xvg=


What point is confusing?

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] NVT NPT restrains

[Justin Lemkul]

On 2/20/18 4:47 PM, Ahmed Mashaly wrote:

Hi Justin
I see the point of restraining heavy atoms in NPT.The problem is that; no posre 
are included in the top file generated by Acpype, any suggestion to overcome 
that? Kind Regards,Ahmed


Write in the directive yourself or generate it with genrestr.

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] About rdf in membranes

[Poncho Arvayo Zatarain]

Hello Gromacs Users: I want to calculate rdf in membranes. I read i need 
something like .xy and i´m a little confussed. The command will be: gmx rdf -f 
file.xtc -s file.tpr -n file.ndx -xy -o file.xvg=

Thanks for your help
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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

What version of GROMACS are you using?  Do you have periodic molecules
in the system? i.e. periodic-molecules = yes in mdp file?

Known bug, that has been recently fixed.

https://redmine.gromacs.org/issues/2275
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 20 February 2018 at 22:27, Iman Ahmadabadi
 wrote:
> Dear Gromacs users,
>
> In using some commands in gromacs, the sentence "There were 240
> inconsistent shifts. Check your topology" come up on the screen and I don't
> know what is wrong in my topology file, however it calculates correctly the
> features of the system but I would like to know the reason of this warning.
>
> Respectfully,
> Iman
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Re: [gmx-users] NVT NPT restrains

[Ahmed Mashaly]

Hi Justin
I see the point of restraining heavy atoms in NPT.The problem is that; no posre 
are included in the top file generated by Acpype, any suggestion to overcome 
that? Kind Regards,Ahmed



  From: Justin Lemkul 
 To: gmx-us...@gromacs.org 
 Sent: Tuesday, February 20, 2018 7:55 PM
 Subject: Re: [gmx-users] NVT NPT restrains
   


On 2/20/18 1:47 PM, Ahmed Mashaly wrote:
> Hi
>
> About the restrains, I see that it is necessary for NVT and NPT.
> For the .top and .gro produced by Acpype,
> https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM
>
> I don't have porse.itp nor anything related to restrain in the .top file, 
> only for water
>
> #ifdef FLEXIBLE
> [ bonds ]
> ; i j  funct  length  force.c.
> 1  2  1  0.09572  462750.4 0.09572  462750.4
> 1  3  1  0.09572  462750.4 0.09572  462750.4
>
>
> So what shall I do in this case? and what is the ideal time for NVT and NPT

Restraints are typically applied to solute heavy atoms to prevent 
distortion from initial, artificial configurations. It is very rare to 
need to restrain water, as that defeats the purpose of equilibration, 
which is primarily to allow the solvent to relax and achieve the desired 
state.

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] users list archive

[Justin Lemkul]

On 2/20/18 1:58 PM, Lovas, Sandor wrote:

For the past several days I am unable to reach/search the users list
archive. I get the following error message when I try to load it:

"Forbidden
You don't have permission to access /pipermail/gromacs.org_gmx-users/
on this server.

Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443"

Is it down?


Yes, it's down. This has been asked and answered a few times.

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] users list archive

[Lovas, Sandor]

For the past several days I am unable to reach/search the users list
archive. I get the following error message whrn I try to load it:

"Forbidden
You don't have permission to access /pipermail/gromacs.org_gmx-users/
on this server.

Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443"

Is it down?
Thanks
Sandor

-- 
__
Dr. Sandor Lovas, Professor
Department of Biomedical Sciences  
Creighton University   
2500 California Plaza, 
Omaha, NE 68178, USA 

Phone: 402-280-5753
Fax:   402-280-2690 
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[gmx-users] users list archive

[Lovas, Sandor]

For the past several days I am unable to reach/search the users list
archive. I get the following error message when I try to load it:

"Forbidden
You don't have permission to access /pipermail/gromacs.org_gmx-users/
on this server.

Apache/2.2.15 (Red Hat) Server at mailman-1.sys.kth.se Port 443"

Is it down?
Thanks
Sandor
-- 
__
Dr. Sandor Lovas, Professor
Department of Biomedical Sciences  
Creighton University   
2500 California Plaza, 
Omaha, NE 68178, USA 

Phone: 402-280-5753
Fax:   402-280-2690 
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Re: [gmx-users] NVT NPT restrains

[Justin Lemkul]

On 2/20/18 1:47 PM, Ahmed Mashaly wrote:

Hi

About the restrains, I see that it is necessary for NVT and NPT.
For the .top and .gro produced by Acpype,
https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM

I don't have porse.itp nor anything related to restrain in the .top file, only 
for water

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572   462750.4 0.09572   462750.4
1   3   1   0.09572   462750.4 0.09572   462750.4


So what shall I do in this case? and what is the ideal time for NVT and NPT


Restraints are typically applied to solute heavy atoms to prevent 
distortion from initial, artificial configurations. It is very rare to 
need to restrain water, as that defeats the purpose of equilibration, 
which is primarily to allow the solvent to relax and achieve the desired 
state.


-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.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 2/20/18 12:52 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD?
  


Precisely what I said, yes.

-Justin



Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting
point for your simulation. Tweaks to emtol will have little to no
noticeable bearing on the conformational ensemble generated by MD.

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] NVT NPT restrains

[Ahmed Mashaly]

Hi

About the restrains, I see that it is necessary for NVT and NPT.
For the .top and .gro produced by Acpype, 
https://drive.google.com/open?id=1K5IqAWb1_jXUfUPDjDtkOX2l8GuzbprM

I don't have porse.itp nor anything related to restrain in the .top file, only 
for water

#ifdef FLEXIBLE
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572   462750.4 0.09572   462750.4
1   3   1   0.09572   462750.4 0.09572   462750.4


So what shall I do in this case? and what is the ideal time for NVT and NPT
 Kind Regards,
Ahmed
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Re: [gmx-users] energy minimization

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the 
conformational enssemble generated by MD? 
 

Sent from Yahoo Mail for iPhone


On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul  wrote:



On 2/20/18 4:52 AM, farial tavakoli wrote:
> Dear GMX users
> I used CHARMM36 all atom force field to generate .top and .gro files for my 
> complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
> residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
> respectively. While, I calculated binding energy before for many other 
> complexes without any phosphate groups using OPLS all atom force field and 
> pdie = 2 and obtained minus energy. But this time , I dont know why I got 
> positive binding energy? Is it because of charmm36 all atom force field , the 
> phosphate groups or it is needed to be energy minimized under more 
> restriction situations?
> I am checking different factors to understand its reason, so I wanted to know 
> , would it be ok if I energy minimize the complex with more restriction 
> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 
> ? I think the positive binding energy might be because of the complex didnt 
> minimized well. however I checked the em.log file and saw it was minimized 
> well:
>
> Steepest Descents converged to Fmax < 1000 in 241 steps
> Potential Energy  = -6.5047744e+05
> Maximum force =  9.8285083e+02 on atom 3335
> Norm of force =  3.6905827e+01
> Is there anyone can advice me in energy minimization with emtol 800?

The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.

-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.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] simulation time vs side chain flexibility

[MD]

Thank you J.
Ming

On Tue, Feb 20, 2018 at 12:29 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> To be honest, I don't see how an increased side chain flexibility is proof
> that the protein is more flexible. They're not necessarily correlated.
> Protein flexibility involves larger movements concerning the protein
> backbone. These would probably be better captured by the RMSF, radius or
> gyration, end-to-end distance, etc.
>
> J
>
> On Tue, Feb 20, 2018 at 6:16 PM, MD  wrote:
>
> > Thanks J. I agree. I should have added that the RMSD plateaued. And I am
> > more looking at side chain flexibility instead of secondary structure
> > changes.
> > Ming
> >
> > On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > This is not strictly a gromacs related question, but long answer short:
> > it
> > > depends, but most likely not. You must be able to convince people that
> > the
> > > property you're interested in is properly converged within the
> simulation
> > > time you're considering. Multiple, reversible events need to be clearly
> > > visible.
> > >
> > > In general, significant protein conformational changes occur at a much
> > > larger time scale (and I'm talking orders of magnitude larger). 10 ns
> is
> > a
> > > very, very short time for most purposes in protein simulation.
> > >
> > > I could go on and on, this is a complex topic that can easily be
> written
> > > about at length.
> > >
> > > J
> > >
> > > On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:
> > >
> > > > Hi Gromacs folks,
> > > >
> > > > I am trying to tell if a mutation can cause some part of the protein
> > > > becoming more flexible. I started with the apo protein. I did two
> > > > simulations in parallel, with one wild type and one with a silico
> > > mutation.
> > > >
> > > > After a 10 ns simulation I was able to tell some region of the
> protein
> > is
> > > > more flexible based on the RMS chart. Since side chain flexibility is
> > in
> > > > the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
> > > >
> > > > Thanks,
> > > >
> > > > Ming
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > >
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Re: [gmx-users] simulation time vs side chain flexibility

[MD]

Thank you Justin.
Ming

On Tue, Feb 20, 2018 at 12:27 PM, Justin Lemkul  wrote:

>
>
> On 2/20/18 12:16 PM, MD wrote:
>
>> Thanks J. I agree. I should have added that the RMSD plateaued. And I am
>>
>
> Don't let RMSD lull you into a false sense of security. If your side chain
> gets "stuck" in one conformation, its RMSD will be low, but it tells you
> nothing about its flexibility because there are no reversible transitions.
> Moreover, RMSD is a degenerate metrics that does not tell you anything
> about the actual convergence of your simulation. It may be a first
> indicator in many cases, but it is not definitive by any means.
>
> RMSF is very sensitive to proper equilibration. I normally discard at
> least 10-20 ns of simulation time before trusting my RMSF results (which
> are then independently monitored for their own convergence in
> non-overlapping windows of time).
>
> -Justin
>
>
> more looking at side chain flexibility instead of secondary structure
>> changes.
>> Ming
>>
>> On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
>> joao.m.a.henriq...@gmail.com> wrote:
>>
>> This is not strictly a gromacs related question, but long answer short: it
>>> depends, but most likely not. You must be able to convince people that
>>> the
>>> property you're interested in is properly converged within the simulation
>>> time you're considering. Multiple, reversible events need to be clearly
>>> visible.
>>>
>>> In general, significant protein conformational changes occur at a much
>>> larger time scale (and I'm talking orders of magnitude larger). 10 ns is
>>> a
>>> very, very short time for most purposes in protein simulation.
>>>
>>> I could go on and on, this is a complex topic that can easily be written
>>> about at length.
>>>
>>> J
>>>
>>> On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:
>>>
>>> Hi Gromacs folks,

 I am trying to tell if a mutation can cause some part of the protein
 becoming more flexible. I started with the apo protein. I did two
 simulations in parallel, with one wild type and one with a silico

>>> mutation.
>>>
 After a 10 ns simulation I was able to tell some region of the protein
 is
 more flexible based on the RMS chart. Since side chain flexibility is in
 the range of 1 ns, I wonder if 10 ns simulation is convincing enough?

 Thanks,

 Ming
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> Justin A. Lemkul, Ph.D.
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>
> 303 Engel Hall
> 340 West Campus Dr.
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>
> jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] 2018 performance question

[Szilárd Páll]

Hi Michael,

What you observe is most likely due to v2018 by default shifting the
PME work to the GPU which will often mean fewer CPU cores are needed
and runs become more GPU-bound leaving the CPU without work for part
of the runtime. This should be easily seen by comparing the log files.

Especially with older GPUs (approx >2 gen old Kepler or earlier)
running only part of the PME work on the GPU can be useful. This can
be done by using the hybrid PME mode that runs 3D-FFT / gather on the
CPU:
gmx mdrun -pmefft cpu

That might give you better CPU/GPU load balance, and sometimes a
moderate performance improvement. Otherwise, there are a few things
you can do to make better overall use of the machine:
- use fewer cores without giving up much performance (e.g. leave 2
cores free for other tasks) -- that's useful if you have other work
you can do on the free cores;
- run multiple runs to fill "utilization gaps": e.g. run 2-3
concurrent runs with 2-3 cores each.

Cheers,
--
Szilárd


On Fri, Feb 16, 2018 at 12:41 PM, Michael Brunsteiner  wrote:
>
> hi
> just installed gmx-2018 on a x86_64 PC with a Geforce GTX 780 and the 
> cudasoftware directly from the nvidia webpage (didn't work using the debian 
> nvidia packages)
> output of lscpu is included below.
> i find that:
> 1) 2018 is slightly faster (~5%) than 2016.2) both 2016 and 2018 use the GPU, 
> but 2018 seems to use less CPU.
> With 2016 using the "top" command i usually see that the CPU load is close to 
> 1200%(i have 6 cores, each two threads) while with 2018 this number is closer 
> to around 400%(I guess this is because 2018 does PME on the GPU)
> my question is: can i possibly further improve the performance of 2018 by1) 
> somehow convincing gmx to use more CPU, or
> 2) run two instances of gmx on this one computer simultaneously??
> thanks in advance for any feedback!
> cheers,Michael
>
>
>
> prompt> lscpuArchitecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):12
> On-line CPU(s) list:   0-11
> Thread(s) per core:2
> Core(s) per socket:6
> Socket(s): 1
> NUMA node(s):  1
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 62
> Model name:Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> Stepping:  4
> CPU MHz:   3399.898
> CPU max MHz:   3900.
> CPU min MHz:   1200.
> BogoMIPS:  6799.79
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  256K
> L3 cache:  12288K
> NUMA node0 CPU(s): 0-11
> Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
> mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx 
> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology 
> nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est 
> tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt 
> tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm epb kaiser tpr_shadow 
> vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts
>
>
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Re: [gmx-users] energy minimization

[Justin Lemkul]

On 2/20/18 4:52 AM, farial tavakoli wrote:

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?


The purpose of energy minimization is to establish a reasonable starting 
point for your simulation. Tweaks to emtol will have little to no 
noticeable bearing on the conformational ensemble generated by MD.


-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
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Re: [gmx-users] Energygrps

[Justin Lemkul]

On 2/20/18 5:49 AM, Ahmed Mashaly wrote:

Hi
What is the default engerygrps to be written if I don't specify them in the mdp 
file?


The default behavior is to not decompose the energy in any fashion, and 
just report it for the whole system.



And if I have more than one ligand and want to calculate the energy between 
them and the protein, and also between one part of the protein (loop) and the 
rest of the protein I should make an index identifying each ligand indvidually 
and this part too and my energygrps will be protein lig1 protein lig2 protein 
loop ...


A real snippet of an .mdp would be good here, because it appears you're 
just repeating groups, which is not appropriate. If you want the 
interaction of a ligand with a protein, use:


energygrps = Protein LIG

If there are multiple groups to consider:

energygrps = Protein LIG1 LIG2

A full matrix of all possible combinations will be generated. Whether or 
not this quantity means anything within a given force field is another 
matter, but I'm a broken record in saying that nearly every day on this 
list.



If I don't specify this from the beginning is it the same to get with mdrun 
rerun or will be different? This


Yes, this is the main purpose of mdrun -rerun. There is no need to bog 
mdrun down with such energy decomposition because the physics doesn't 
depend on it. Treat it as analysis and just get the values by 
post-processing the trajectory.


-Justin

--
==

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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.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] simulation time vs side chain flexibility

[João Henriques]

To be honest, I don't see how an increased side chain flexibility is proof
that the protein is more flexible. They're not necessarily correlated.
Protein flexibility involves larger movements concerning the protein
backbone. These would probably be better captured by the RMSF, radius or
gyration, end-to-end distance, etc.

J

On Tue, Feb 20, 2018 at 6:16 PM, MD  wrote:

> Thanks J. I agree. I should have added that the RMSD plateaued. And I am
> more looking at side chain flexibility instead of secondary structure
> changes.
> Ming
>
> On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > This is not strictly a gromacs related question, but long answer short:
> it
> > depends, but most likely not. You must be able to convince people that
> the
> > property you're interested in is properly converged within the simulation
> > time you're considering. Multiple, reversible events need to be clearly
> > visible.
> >
> > In general, significant protein conformational changes occur at a much
> > larger time scale (and I'm talking orders of magnitude larger). 10 ns is
> a
> > very, very short time for most purposes in protein simulation.
> >
> > I could go on and on, this is a complex topic that can easily be written
> > about at length.
> >
> > J
> >
> > On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:
> >
> > > Hi Gromacs folks,
> > >
> > > I am trying to tell if a mutation can cause some part of the protein
> > > becoming more flexible. I started with the apo protein. I did two
> > > simulations in parallel, with one wild type and one with a silico
> > mutation.
> > >
> > > After a 10 ns simulation I was able to tell some region of the protein
> is
> > > more flexible based on the RMS chart. Since side chain flexibility is
> in
> > > the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
> > >
> > > Thanks,
> > >
> > > Ming
> > > --
> > > 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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Re: [gmx-users] Calculate RDF within a certain distance from atom

[Justin Lemkul]

On 2/20/18 11:53 AM, Dilip H N wrote:

Hello,
How to get RDF within a certain distance..??

Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
atoms within 0.7nm of C-alpha (Calpha-Ow).

how can i get it from in-house gmx rdf command...??


What do you hope to achieve from such a metric? RDF has to be normalized 
against bulk occupancy, which will of course not be achieved at a 0.7-nm 
distance. If you are interested in certain properties within given 
solvation shells, distances, etc. compute the normal RDF so that it is 
properly normalized and interpret the outcome of that calculation.


-Justin

--
==

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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
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Re: [gmx-users] simulation time vs side chain flexibility

[Justin Lemkul]

On 2/20/18 12:16 PM, MD wrote:

Thanks J. I agree. I should have added that the RMSD plateaued. And I am


Don't let RMSD lull you into a false sense of security. If your side 
chain gets "stuck" in one conformation, its RMSD will be low, but it 
tells you nothing about its flexibility because there are no reversible 
transitions. Moreover, RMSD is a degenerate metrics that does not tell 
you anything about the actual convergence of your simulation. It may be 
a first indicator in many cases, but it is not definitive by any means.


RMSF is very sensitive to proper equilibration. I normally discard at 
least 10-20 ns of simulation time before trusting my RMSF results (which 
are then independently monitored for their own convergence in 
non-overlapping windows of time).


-Justin


more looking at side chain flexibility instead of secondary structure
changes.
Ming

On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:


This is not strictly a gromacs related question, but long answer short: it
depends, but most likely not. You must be able to convince people that the
property you're interested in is properly converged within the simulation
time you're considering. Multiple, reversible events need to be clearly
visible.

In general, significant protein conformational changes occur at a much
larger time scale (and I'm talking orders of magnitude larger). 10 ns is a
very, very short time for most purposes in protein simulation.

I could go on and on, this is a complex topic that can easily be written
about at length.

J

On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:


Hi Gromacs folks,

I am trying to tell if a mutation can cause some part of the protein
becoming more flexible. I started with the apo protein. I did two
simulations in parallel, with one wild type and one with a silico

mutation.

After a 10 ns simulation I was able to tell some region of the protein is
more flexible based on the RMS chart. Since side chain flexibility is in
the range of 1 ns, I wonder if 10 ns simulation is convincing enough?

Thanks,

Ming
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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

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Re: [gmx-users] simulation time vs side chain flexibility

[MD]

Thanks J. I agree. I should have added that the RMSD plateaued. And I am
more looking at side chain flexibility instead of secondary structure
changes.
Ming

On Tue, Feb 20, 2018 at 12:09 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> This is not strictly a gromacs related question, but long answer short: it
> depends, but most likely not. You must be able to convince people that the
> property you're interested in is properly converged within the simulation
> time you're considering. Multiple, reversible events need to be clearly
> visible.
>
> In general, significant protein conformational changes occur at a much
> larger time scale (and I'm talking orders of magnitude larger). 10 ns is a
> very, very short time for most purposes in protein simulation.
>
> I could go on and on, this is a complex topic that can easily be written
> about at length.
>
> J
>
> On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:
>
> > Hi Gromacs folks,
> >
> > I am trying to tell if a mutation can cause some part of the protein
> > becoming more flexible. I started with the apo protein. I did two
> > simulations in parallel, with one wild type and one with a silico
> mutation.
> >
> > After a 10 ns simulation I was able to tell some region of the protein is
> > more flexible based on the RMS chart. Since side chain flexibility is in
> > the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
> >
> > Thanks,
> >
> > Ming
> > --
> > 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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Re: [gmx-users] simulation time vs side chain flexibility

[João Henriques]

This is not strictly a gromacs related question, but long answer short: it
depends, but most likely not. You must be able to convince people that the
property you're interested in is properly converged within the simulation
time you're considering. Multiple, reversible events need to be clearly
visible.

In general, significant protein conformational changes occur at a much
larger time scale (and I'm talking orders of magnitude larger). 10 ns is a
very, very short time for most purposes in protein simulation.

I could go on and on, this is a complex topic that can easily be written
about at length.

J

On Tue, Feb 20, 2018 at 5:48 PM, MD  wrote:

> Hi Gromacs folks,
>
> I am trying to tell if a mutation can cause some part of the protein
> becoming more flexible. I started with the apo protein. I did two
> simulations in parallel, with one wild type and one with a silico mutation.
>
> After a 10 ns simulation I was able to tell some region of the protein is
> more flexible based on the RMS chart. Since side chain flexibility is in
> the range of 1 ns, I wonder if 10 ns simulation is convincing enough?
>
> Thanks,
>
> Ming
> --
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[gmx-users] Calculate RDF within a certain distance from atom

[Dilip H N]

Hello,
How to get RDF within a certain distance..??

Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
atoms within 0.7nm of C-alpha (Calpha-Ow).

how can i get it from in-house gmx rdf command...??

Any suggestions are appreciated...

Thank you.


-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



‌
 Sent with Mailtrack

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[gmx-users] simulation time vs side chain flexibility

[MD]

Hi Gromacs folks,

I am trying to tell if a mutation can cause some part of the protein
becoming more flexible. I started with the apo protein. I did two
simulations in parallel, with one wild type and one with a silico mutation.

After a 10 ns simulation I was able to tell some region of the protein is
more flexible based on the RMS chart. Since side chain flexibility is in
the range of 1 ns, I wonder if 10 ns simulation is convincing enough?

Thanks,

Ming
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Re: [gmx-users] How to obtain TIP4P/ε water model topology file

[João Henriques]

I'm not very familiar with the TIP4P/ε water model, but if my memory serves
me correctly, isn't it meant for pure water simulations? I'm not sure it's
a good idea to mix it up with a protein force field without proper testing.
Also, CHARMM36 was parametrized to be used with the CHARMM-modified TIP3P
water model, so that makes it even more risky. In any case, I doubt
CHARMM36 comes packaged with it, you'll probably have to create it yourself.

J

On Tue, Feb 20, 2018 at 5:30 PM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi All,
> I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let
> me know where can I get the corresponding .itp file.
>
> Thanks a lot.
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
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Re: [gmx-users] Worse GROMACS performance with better specs?

[Szilárd Páll]

On Fri, Jan 12, 2018 at 2:35 AM, Jason Loo Siau Ee
 wrote:
> Dear Carsten,
>
> Look's like we're seeing the same thing here, but only when using gcc 4.5.3:
>
> Original performance (gcc 5.3.1, AVX512, no hwloc support): 49 ns/day
>
> With hwloc support:
> gcc 4.5.3, AVX2_256 = 67 ns/day
> gcc 4.5.3, AVX512 = can't compile
> gcc 5.3.1, AVX2_256 = 36 ns/day
> gcc 5.3.1, AVX512 = 60 ns/day
>
> At the very least it's now comparable to my previous workstation. Will have 
> to try with the gromacs 2018 next.

Have you tried? Any feedback?

I'd also recommend using gcc >=6.

>
> Cheers for the info.
>
> Jason
>
> --
>
> Message: 2
> Date: Wed, 10 Jan 2018 08:39:22 +
> From: "Kutzner, Carsten" 
> To: " GROMACS users" 
> Subject: Re: [gmx-users] Worse GROMACS performance with better specs?
> Message-ID: <816dea54-1e01-42ac-a78a-3680fdef0...@gwdg.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Jason,
>
> 1.)
> we have observed a similar behavior comparing Intel Silver 4114 against 
> E5-2630v4
> processors in a server with one GTX 1080Ti. Both CPUs have 10 cores and run at
> 2.2 GHz. Using our standard benchmark systems (see 
> https://arxiv.org/abs/1507.00898)
> we were able to get 74.4 ns/day on the E5 but only 65.7 ns/day on the Silver 
> machine
> for the MEM (80k atoms), and 4.4 vs. 4.2 ns/day for the RIB (2M atoms) system.
>
> Although the 4114 supports AVX512 SIMD instructions, compiling with AVX2_256
> yielded higher performance (this is already included in the above numbers, so
> all benchmarks were run with the exact same mdrun executable).
>
> 2.)
> We recently bought a bunch of workstations with 2x Gold 6146 CPUs and 2x 
> GTX1080Ti GPUs
> and were very surprised to find that initial GROMACS 2016 performances differ 
> a
> lot between the identical machines (some were up to 40% slower).
>
> This was the reported difference in the md.log files:
>> - mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only 
>> logical processor count
>
>
> For some reason, the logical processor count was reported in a mixed-up way
> for the slower machines so that mdrun is unable to correctly determine the
> hardware topology. We solved this CPU problem by installing GROMACS with hwloc
> support. Then performances were equal over all 6146 nodes.
>
> Best,
>   Carsten
>
>
>> On 10. Jan 2018, at 07:45, Jason Loo Siau Ee 
>>  wrote:
>>
>> Dear gmx users,
>>
>>
>>
>> I recently purchased a second GPU workstation and tried compiling GROMACS on 
>> it, but despite the better (and more expensive) specs the performance is 
>> significantly worse on my test system. To test things I standardized the 
>> version (2016.4). Some details below:
>>
>>
>>
>> Workstation 1:
>>
>> 2 x Intel Xeon E5-2680v4 (14 cores), 2 x GTX 1080
>>
>> gmx mdrun -ntmpi 8 -ntomp 7 -gpu_id 
>>
>> Performance: 61ns/day
>>
>>
>>
>> Workstation 2:
>>
>> 2 x Intel Xeon Gold 6126 (12 cores), 2 x GTX 1080Ti
>>
>> gmx mdrun -ntmpi 8 -ntomp 6 -gpu_id 
>>
>> Performance: 49ns/day
>>
>>
>>
>> I'm guessing it's an issue during compilation but I can't figure it out. I 
>> wouldn't claim to have any knowledge about how GROMACS interacts with the 
>> hardware, so some observations as below (not sure idea which is actually 
>> relevant):
>>
>>
>>
>> - Compilation command for both: cmake .. -DGMX_BUILD_OWN_FFTW=ON  
>> -DREGRESSIONTEST_DOWNLOAD=ON  -DGMX_GPU=ON  
>> -DCMAKE_INSTALL_PREFIX=/opt/gromacs
>>
>>
>>
>> - When compiling on Workstation 2 I originally got a CMake error "Cannot 
>> find AVX512F compiler flag". Updated my gcc version to 5.3.1 to solve this.
>>
>>
>>
>> - Some regression tests fail for Workstation 2 during compilation: 4 
>> -FTUnitTest (SEGFAULT), 16 - CorrelationTest
>>
>>
>>
>> - mdrun logs show Hardware Topology: Basic versus Hardware Topology: Only 
>> logical processor count
>>
>>
>>
>> - Running CPU-only (export CUDA_VISIBLE_DEVICES="") I get 21ns/day versus 23 
>> ns/day , so the CPUs in Workstation 2 are definitely faster.
>>
>>
>>
>> - Upgraded both to 2018.rc1 (used cmake3) I get a regression test fail for 
>> Workstation 1 (9 - GPUUtilUnitTest) and Workstation 2 (8 - FFTUnitTests, 9 - 
>> GPUUtilsUnitTest, 26 - CorrelationTest). Performance is 66.5ns/day versus 
>> 51.95ns/day. The GPU load actually looks similar to previous versions (~70% 
>> for Workstation 1 and 50-60% for Workstation 2). I actually got the best 
>> performance with Workstation 1 running 2016.1 (69ns/day).
>>
>>
>>
>> Any help on how I can optimize performance on Workstation 2 would be 
>> appreciated. If there are certain files that would be helpful let me know 
>> and I'll send a link.
>>
>>
>>
>> Cheers,
>> Jason
>>
>>
>>
>>
>>
>>
>>
>> Jason Loo
>>
>> PhD, MPharm, RPh
>>
>> Lecturer
>>
>> School of Pharmacy
>>
>> Faculty of Health and Medical Sciences
>>
>> Taylor's University
>>
>>
>>
>> This message (including any attachments) is intended only for
>> the use of the individual or entity to whi

[gmx-users] multi-replica runs with GPUs [fork of Re: Gromacs 2018 and GPU PME ]

[Szilárd Páll]

Hi Dan,

On Fri, Feb 9, 2018 at 4:56 PM, Daniel Kozuch  wrote:

> Szilárd,
>
> If I may jump in on this conversation,



Let's fork the thread so the topics stay clear and discoverable by others,
please.

I am having the reverse problem
> (which I assume others may encounter also) where I am attempting a large
> REMD run (84 replicas) and I have access to say 12 GPUs and 84 CPUs.
>

OK. That's a useful case to clarify. If you have exactly 84 CPUs for your
84 runs and as that number of divisible by the number of GPUs too, it
should be as simple as running
mpirun -np 84 gmx_mpi mdrun -multi 84
and the automatic mapping of ranks/threads to hardware should work just
fine.

Basically I have less GPUs than simulations. Is there a logical approach to
> using gputasks and other new options in GROMACS 2018 for this setup? I read
> through the available documentation,but as you mentioned it seems to be
> targeted for a single-GPU runs.
>


TL;DR
Correction: PME GPU offload is tuned for single-GPU (more precisely
domain-decomposition) simulations. The -gpu_id/-gputasks options have been
fairly well thought through to be useful for all current and most future
use-cases ;) Therefore, the use of -gputasks is valid and useful in
multi-rank and multi-sim/replica runs as well: it will still map GPUs to
tasks/rank within a node.


You'll find a bit more detailed writeup below which might refresh & clarify
the details of mdrun internal workings.




First a brief recap of the basics (for those inexperienced or needing a
reminder):
GROMACS uses heterogeneous offload parallelization, i.e. CPU & GPU are both
used. This has a number of benefits and drawbacks, what is relevant in this
context is that for a highly tuned MD engine it is generally difficult to
achieve perfect load balance and 100% utilization of both CPU and GPU (in
fact the same applies to ranks of an MPI-parallel run). Consequently, part
of the runtime will be spent waiting for the GPU on the CPU or vice-versa.
GPUs are easy to share among multiple, dependent or independent jobs
(unlike CPUs/cores) and this can help make use of otherwise idle GPU time.
By setting up threads/processes to share GPUs (e.g. ranks in a multi-sim
run or even independent program executions), these can fill the GPU
utilization "gaps" generally resulting in better overall efficiency, e.g.
higher aggregate ns/day. GPU sharing has a moderate importance in
multi-GPU/node parallel runs (i.e. it is useful to run a few ranks per
GPU), but even more important in throughput type use with a few to many
independent runs -- as a reminder, we've talked about this in our paper and
most information is still useful and valid, see Fig 5 and related
discussion of https://goo.gl/FvkGC7


Back to the use of -gpu_id / -gputasks. The slight change is that the roles
of -gpu_id have been separated: previously it specified *both* the IDs of
the devices to use as well as the mapping of the devices to the tasks/ranks
in a simulation. In the 2018 release -gpu_id *only specifies which devices
to use*, while -gputasks provides the mapping (and it is in most cases
optional).
E.g. these three are equivalent, but the former is not valid in v2018
mdrun -ntmpi 4 -gpu_id 0011 -nb gpu # map two GPUs to four ranks in v2016
mdrun -ntmpi 4 [-gpu_id 01] -gputasks 0011 -nb gpu [-pme cpu] # use GPU 0
and 1 and map two-by-two to the four PP ranks -- in v2018
mdrun -ntmpi 4 # lazy default for both v2016 and v2018 -- assuming there
are only two GPUs and given that PME runs on the CPU by default with DD

Now to PME-GPU: before v2018 there was only a single task type offloaded,
so -gpu_id mapped GPUs to PP tasks within a node (combined PP+PME or
separate PP ranks); for multiple ranks using the same GPU, the ID was
simply repeated. With the additional PME task to offload (which can
"reside" either in the same rank as the PP task or in a separate rank) the
mapping has to account for PME too. What may not be crystal clear from the
docs is that the order of tasks is generally PP first, PME next (both
within a rank and across ranks); also PME ranks are by default interleaved
(unless changed with -ddorder) so in an 8-rank 6 PP / 2 PME setup the rank
order is  3 PP / 1 PME / 3 PP / 1 PME (this is however not supported with
GPUs!)

A few examples leading up to the multi-replica runs:
* a single GPU / single rank run
gmx mdrun -ntmpi 1 -gputasks 00 -nb gpu -pme gpu # verbose command line
gmx mdrun -ntmpi 1 -gpu_id 0 # will do the same as above
gmx mdrun -ntmpi 1 # will also do the same as above ;)

* single node 2 GPUs with separate PME -- note the limitations of this mode
offload mode discussed previously (the mail I've just forked!)
gmx mdrun [-pme gpu -nb gpu] -ntmpi 8 -ntomp 6 -npme 1 -gputasks 0001 #
assuming 24 cores / 48 threads / 2 GPUs
gmx mdrun [-pme gpu -nb gpu] -ntmpi 12 -ntomp 4 -npme 1 -gputasks
0011 # could be more efficient than the above

* single node 2 GPUs 4 replicas 1 rank each 2-way sharing
mpirun -np 4 gmx

[gmx-users] How to obtain TIP4P/ε water model topology file

[Tushar Ranjan Moharana]

Hi All,
I want to use TIP4P/ε water model with CHARMM36 force field. Can anyone let
me know where can I get the corresponding .itp file.

Thanks a lot.

"A society with free knowledge is better than a society with free food"
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

[Mark Abraham]

Hi,

The simplest explanation is that the check is missing that factor, but we
don't yet know that you have tested that the computed forces agree with
your intention in the construction of the table. The computed energies are
not an adequate test. To do that, you need to write the forces using an
.mdp file with nstfout set, and that is best done via mdrun -rerun as I
suggested.

Mark

On Tue, Feb 20, 2018 at 3:49 PM Douwe Pollmann 
wrote:

> Dear Mark,
>
> Thanks for your reaction!
> I have put the dihedral in a test system, where I freeze the positions of
> the atoms and calculate the energy of the system with the Tab.-Dih. option
> in gmx energy.
> The only dihedral in the system is  the one from my own table, and the
> values are in pretty good agreement (deviations of a few percent) with the
> values I would expect.
> So it seems that the interpolation is done correctly, but the strange thing
> is that I still get the warning that the forces deviate on average 196%.
> On one side it is positive that the dihedral energies are correct, but I
> still don't know what the issue is concerning the warning..
> Do you (or someone else) have any other ideas about it?
>
> Best,
> Douwe
>
>
> 2018-02-20 11:20 GMT+01:00 Mark Abraham :
>
> > Hi,
> >
> > It looks like somebody is missing a factor of 2; either you, or the check
> > in the table code, or maybe also in the evaluation kernel. I suggest you
> > set up a three-particle system, and make some coordinate files with those
> > particles at carefully chosen angles and see what energy and force is
> > returned by
> >
> > mdrun -s your.tpr -table yourtable.xvg -rerun your.gro
> >
> > Halve the values in the force column if you have to in order to get a
> force
> > output and understand what the issue really is.
> >
> > Mark
> >
> > On Tue, Feb 20, 2018 at 10:37 AM Douwe Pollmann  >
> > wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am currently trying to implement a user-defined dihedral into a
> coarse
> > > grained model (in version 5.1.4), but I get the following error:
> > >
> > > 'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the
> > > forces deviate on average 196% from minus the numerical derivative of
> the
> > > potential'.
> > >
> > > The three columns in table_d4 are the angle [-180, 180], the potential
> > > energy (in kJ/mol) and minus the derivative (first I had +derivative,
> > which
> > > resulted in an error or 204%). If I am correct, Gromacs interpolates
> its
> > > own function through the data points given in table_d4, but the result
> is
> > > far from correct in this case.
> > >
> > > I have tried to use -debug during mdrun to get the interpolated values
> of
> > > Gromacs, but I only get the values (ctab.xvg, dtab.xvg and rtab.xvg) of
> > the
> > > non-bonded potentials, while this dihedral is of course a bonded
> > potential.
> > >
> > > In section 6.10.1 of the manual (version 5.1.4) it is mentioned that
> > > 'Gromacs stores A0, A1, A2 and A3', the parameters of the interpolated
> > > cubic spline. My question is if any of you knows if it is possible to
> get
> > > these parameters, or if it is possible to get the functions
> interpolated
> > by
> > > Gromacs, to check where the mistakes are made.
> > > If this is not possible at all, do you have any ideas how I can
> decrease
> > > the deviation of the forces? 0% deviation is not needed, but 200% is a
> > bit
> > > too much..
> > >
> > > Thank you very much in advance!
> > >
> > > Kind regards,
> > > Douwe Pollmann
> > > --
> > > 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.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> >
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Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

[Douwe Pollmann]

Dear Mark,

Thanks for your reaction!
I have put the dihedral in a test system, where I freeze the positions of
the atoms and calculate the energy of the system with the Tab.-Dih. option
in gmx energy.
The only dihedral in the system is  the one from my own table, and the
values are in pretty good agreement (deviations of a few percent) with the
values I would expect.
So it seems that the interpolation is done correctly, but the strange thing
is that I still get the warning that the forces deviate on average 196%.
On one side it is positive that the dihedral energies are correct, but I
still don't know what the issue is concerning the warning..
Do you (or someone else) have any other ideas about it?

Best,
Douwe


2018-02-20 11:20 GMT+01:00 Mark Abraham :

> Hi,
>
> It looks like somebody is missing a factor of 2; either you, or the check
> in the table code, or maybe also in the evaluation kernel. I suggest you
> set up a three-particle system, and make some coordinate files with those
> particles at carefully chosen angles and see what energy and force is
> returned by
>
> mdrun -s your.tpr -table yourtable.xvg -rerun your.gro
>
> Halve the values in the force column if you have to in order to get a force
> output and understand what the issue really is.
>
> Mark
>
> On Tue, Feb 20, 2018 at 10:37 AM Douwe Pollmann 
> wrote:
>
> > Dear Gromacs users,
> >
> > I am currently trying to implement a user-defined dihedral into a coarse
> > grained model (in version 5.1.4), but I get the following error:
> >
> > 'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the
> > forces deviate on average 196% from minus the numerical derivative of the
> > potential'.
> >
> > The three columns in table_d4 are the angle [-180, 180], the potential
> > energy (in kJ/mol) and minus the derivative (first I had +derivative,
> which
> > resulted in an error or 204%). If I am correct, Gromacs interpolates its
> > own function through the data points given in table_d4, but the result is
> > far from correct in this case.
> >
> > I have tried to use -debug during mdrun to get the interpolated values of
> > Gromacs, but I only get the values (ctab.xvg, dtab.xvg and rtab.xvg) of
> the
> > non-bonded potentials, while this dihedral is of course a bonded
> potential.
> >
> > In section 6.10.1 of the manual (version 5.1.4) it is mentioned that
> > 'Gromacs stores A0, A1, A2 and A3', the parameters of the interpolated
> > cubic spline. My question is if any of you knows if it is possible to get
> > these parameters, or if it is possible to get the functions interpolated
> by
> > Gromacs, to check where the mistakes are made.
> > If this is not possible at all, do you have any ideas how I can decrease
> > the deviation of the forces? 0% deviation is not needed, but 200% is a
> bit
> > too much..
> >
> > Thank you very much in advance!
> >
> > Kind regards,
> > Douwe Pollmann
> > --
> > 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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[gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Gromacs users,

In using some commands in gromacs, the sentence "There were 240
inconsistent shifts. Check your topology" come up on the screen and I don't
know what is wrong in my topology file, however it calculates correctly the
features of the system but I would like to know the reason of this warning.

Respectfully,
Iman
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[gmx-users] Energygrps

[Ahmed Mashaly]

Hi
What is the default engerygrps to be written if I don't specify them in the mdp 
file?
And if I have more than one ligand and want to calculate the energy between 
them and the protein, and also between one part of the protein (loop) and the 
rest of the protein I should make an index identifying each ligand indvidually 
and this part too and my energygrps will be protein lig1 protein lig2 protein 
loop ...
If I don't specify this from the beginning is it the same to get with mdrun 
rerun or will be different? This questions might have been answered before in 
archive, but there is a problem to access it, any idea when will it be resolved?
Kind Regards,Ahmed 

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Re: [gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

[Mark Abraham]

Hi,

It looks like somebody is missing a factor of 2; either you, or the check
in the table code, or maybe also in the evaluation kernel. I suggest you
set up a three-particle system, and make some coordinate files with those
particles at carefully chosen angles and see what energy and force is
returned by

mdrun -s your.tpr -table yourtable.xvg -rerun your.gro

Halve the values in the force column if you have to in order to get a force
output and understand what the issue really is.

Mark

On Tue, Feb 20, 2018 at 10:37 AM Douwe Pollmann 
wrote:

> Dear Gromacs users,
>
> I am currently trying to implement a user-defined dihedral into a coarse
> grained model (in version 5.1.4), but I get the following error:
>
> 'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the
> forces deviate on average 196% from minus the numerical derivative of the
> potential'.
>
> The three columns in table_d4 are the angle [-180, 180], the potential
> energy (in kJ/mol) and minus the derivative (first I had +derivative, which
> resulted in an error or 204%). If I am correct, Gromacs interpolates its
> own function through the data points given in table_d4, but the result is
> far from correct in this case.
>
> I have tried to use -debug during mdrun to get the interpolated values of
> Gromacs, but I only get the values (ctab.xvg, dtab.xvg and rtab.xvg) of the
> non-bonded potentials, while this dihedral is of course a bonded potential.
>
> In section 6.10.1 of the manual (version 5.1.4) it is mentioned that
> 'Gromacs stores A0, A1, A2 and A3', the parameters of the interpolated
> cubic spline. My question is if any of you knows if it is possible to get
> these parameters, or if it is possible to get the functions interpolated by
> Gromacs, to check where the mistakes are made.
> If this is not possible at all, do you have any ideas how I can decrease
> the deviation of the forces? 0% deviation is not needed, but 200% is a bit
> too much..
>
> Thank you very much in advance!
>
> Kind regards,
> Douwe Pollmann
> --
> 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] energy minimization

[farial tavakoli]

Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my 
complex composed of a receptor protein and a ligand with 2 phosphotyrosine 
residues, then ran a md simulation on it and then used g_mmpbsa to calculate 
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, 
respectively. While, I calculated binding energy before for many other 
complexes without any phosphate groups using OPLS all atom force field and pdie 
= 2 and obtained minus energy. But this time , I dont know why I got positive 
binding energy? Is it because of charmm36 all atom force field , the phosphate 
groups or it is needed to be energy minimized under more restriction 
situations? 
I am checking different factors to understand its reason, so I wanted to know , 
would it be ok if I energy minimize the complex with more restriction 
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? 
I think the positive binding energy might be because of the complex didnt 
minimized well. however I checked the em.log file and saw it was minimized well:

Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy  = -6.5047744e+05
Maximum force =  9.8285083e+02 on atom 3335
Norm of force =  3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800? 
Thank in advanceFarial

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[gmx-users] For non-zero entries for table x, the forces deviate from minus the numerical derivative of the potential

[Douwe Pollmann]

Dear Gromacs users,

I am currently trying to implement a user-defined dihedral into a coarse
grained model (in version 5.1.4), but I get the following error:

'For the 35988 non-zero entries for table 0 in tables/table_d4.xvg the
forces deviate on average 196% from minus the numerical derivative of the
potential'.

The three columns in table_d4 are the angle [-180, 180], the potential
energy (in kJ/mol) and minus the derivative (first I had +derivative, which
resulted in an error or 204%). If I am correct, Gromacs interpolates its
own function through the data points given in table_d4, but the result is
far from correct in this case.

I have tried to use -debug during mdrun to get the interpolated values of
Gromacs, but I only get the values (ctab.xvg, dtab.xvg and rtab.xvg) of the
non-bonded potentials, while this dihedral is of course a bonded potential.

In section 6.10.1 of the manual (version 5.1.4) it is mentioned that
'Gromacs stores A0, A1, A2 and A3', the parameters of the interpolated
cubic spline. My question is if any of you knows if it is possible to get
these parameters, or if it is possible to get the functions interpolated by
Gromacs, to check where the mistakes are made.
If this is not possible at all, do you have any ideas how I can decrease
the deviation of the forces? 0% deviation is not needed, but 200% is a bit
too much..

Thank you very much in advance!

Kind regards,
Douwe Pollmann
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Re: [gmx-users] Graphene simulation, regarding

[RAHUL SURESH]

Dear Alex

Thank you

On Tue, 20 Feb 2018 at 1:59 PM, Alex  wrote:

> This requires custom work, if you are determined to use Gromacs.
>
> If you actually read Andrea's full tutorial
> (http://chembytes.wikidot.com/grocnt), it fully describes the basic
> concept, so then it is fairly clear how to proceed preparing files for
> x2top and then using it. For reduced GO you simply have to add the
> parameters (both bonded and non-bonded) for the hydroxyls similarly to
> how carbons are treated.
>
> Alex
>
>
> On 2/20/2018 12:24 AM, RAHUL SURESH wrote:
> > Dear all,
> >
> > Greetings. I want to perform a simulation of bilayer reduced graphene
> oxide
> > in opls ff. The difficulty is to generate the topology file for the
> bilayer
> > graphene oxide. Andrea Minoia's tutorial gives information only about the
> > planar graphene sheets and nanotubes. How can I develop a valid topology
> > for a bilayer graphene?
> >
> >
> >
> >
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Graphene simulation, regarding

[Alex]

This requires custom work, if you are determined to use Gromacs.

If you actually read Andrea's full tutorial 
(http://chembytes.wikidot.com/grocnt), it fully describes the basic 
concept, so then it is fairly clear how to proceed preparing files for 
x2top and then using it. For reduced GO you simply have to add the 
parameters (both bonded and non-bonded) for the hydroxyls similarly to 
how carbons are treated.


Alex


On 2/20/2018 12:24 AM, RAHUL SURESH wrote:

Dear all,

Greetings. I want to perform a simulation of bilayer reduced graphene oxide
in opls ff. The difficulty is to generate the topology file for the bilayer
graphene oxide. Andrea Minoia's tutorial gives information only about the
planar graphene sheets and nanotubes. How can I develop a valid topology
for a bilayer graphene?






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