Re: [gmx-users] using enegygrps

[kordzadeh]

Hi Dr.Lemkul

Thank you very much for your answer and your time

 I m using Gromos 54a7 force field, How can I find my force field is 
parametrized in such a way that the nonbonded energy decomposition has some 
physical meaning?

Thank you

Regards

Azadeh

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Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

[Justin Lemkul]

On 2/14/18 5:28 PM, Easton J.W. wrote:

Hi Justin,

Many thanks for the detailed reply.

I just wanted to check that it doesn't matter that the A2C and A3C are not 
present in the bonded and non-bonded itp files for the forcefield? Should this 
not have given an error?


The topology snippet you showed an [atomtypes] directive with those 
types defined, so they were in fact in the nonbonded parameter list by 
virtue of being added just above the first [moleculetype], as is 
permitted in GROMACS topologies. If there were missing parameters, 
grompp would have failed with a fatal error, so presumably you also 
included the necessary bonded parameters somewhere, too.


-Justin


Kind regards,

James

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

Sent: 14 February 2018 14:43:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 9:42 AM, Justin Lemkul wrote:


On 2/14/18 9:33 AM, Easton J.W. wrote:

Thanks Justin,


Will this effect the interactions (both bonded and non-bonded) that
these atoms have, as their atom types are not in the forcefield itp
files?

Missing atom types would cause grompp to fail; you'd never get to the
point where a simulation would be affected.

You're introducing custom atom types in the topology itself, and
that's always legal before any [moleculetype] appears. The LJ
parameters come from the [atomtypes] directive. Masses and charges
present in that directive aren't used.


Actually, to clarify: *if* masses are present in the [atoms] directive
of a [moleculetype], then the masses found in [atomtypes] are not used.
Strictly speaking, it is not necessary to have explicit masses in
[atoms], though nearly all topologies do.

-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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Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

[Easton J . W .]

Hi Justin,

Many thanks for the detailed reply.

I just wanted to check that it doesn't matter that the A2C and A3C are not 
present in the bonded and non-bonded itp files for the forcefield? Should this 
not have given an error?

Kind regards,

James

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

Sent: 14 February 2018 14:43:35
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 9:42 AM, Justin Lemkul wrote:
>
>
> On 2/14/18 9:33 AM, Easton J.W. wrote:
>> Thanks Justin,
>>
>>
>> Will this effect the interactions (both bonded and non-bonded) that
>> these atoms have, as their atom types are not in the forcefield itp
>> files?
>
> Missing atom types would cause grompp to fail; you'd never get to the
> point where a simulation would be affected.
>
> You're introducing custom atom types in the topology itself, and
> that's always legal before any [moleculetype] appears. The LJ
> parameters come from the [atomtypes] directive. Masses and charges
> present in that directive aren't used.
>

Actually, to clarify: *if* masses are present in the [atoms] directive
of a [moleculetype], then the masses found in [atomtypes] are not used.
Strictly speaking, it is not necessary to have explicit masses in
[atoms], though nearly all topologies do.

-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] Flexible and posres

[Justin Lemkul]

On 2/14/18 2:47 PM, Iman Ahmadabadi wrote:

Dear Justin,

Because there is a movement on atoms that posres should act on them, and
this condition doesn't occur when the flexible option is not used.


Restraints don't prevent movement, only disfavor it. Have you quantified 
this in any way? RMSD? Is there a "Position Rest." energy term written 
to your log file? If so, the restraints are there and acting, but maybe 
you need a different force constant.


-Justin


Sincerely,
Iman

On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi  wrote:


Dear Gromacs Users,

If I wanna use some flexible bonds and also use position restraint on
some other atoms, how should I do this? the error arises because 2 define =
-DFLEXIBLE and -POSRES is not allowed in the .mdp files.

Respectfully




--
==

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] Flexible and posres

[Iman Ahmadabadi]

Dear Justin,

Because there is a movement on atoms that posres should act on them, and
this condition doesn't occur when the flexible option is not used.

Sincerely,
Iman

On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi  wrote:

> Dear Mark,
>
> I forgot the D in -DPOSRES in the previous email. However I used the
> "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
> was not applied on the atoms. Is there another way to solve the problem?
>
> Respectfully,
> Iman
>
> On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs Users,
>>
>> If I wanna use some flexible bonds and also use position restraint on
>> some other atoms, how should I do this? the error arises because 2 define =
>> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>>
>> Respectfully
>>
>>
>
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Re: [gmx-users] using enegygrps

[Justin Lemkul]

On 2/14/18 1:15 PM, kordza...@aut.ac.ir wrote:

Hi all

I want to investigate interaction drug and bilayer for more detailed 
investigation I want to use energygrps for functional group of drug to find out 
which part of drug has more interaction.

is energygrps good tool?


If the force field you're using was parametrized in such a way that the 
nonbonded energy decomposition has some physical meaning, maybe. But 
chopping a molecule into pieces and calculating pairwise nonbonded 
energies is not a useful approach. An entire molecule, for the purpose 
of comparison, maybe.


-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] pressure coupling error in umbrella sampling

[Justin Lemkul]

On 2/14/18 1:06 PM, kordza...@aut.ac.ir wrote:

Hi Dr.Lemkul

Thank you very much for your answer

I get it now, before your answer I run system with -maxwarn 1, I saw trajectory 
in vmd , my drug molecule break in middle of run and then corrected, is it 
wrong?


No, that's called periodic boundary conditions.


has it occured because using maxwran?


No.


is vmd an appropriate tool for detect trajectory?


You can use whatever visualization software you like, but you should use 
trjconv first to get a consistent, intact representation.



I alaways after run, check trajectory with vmd to sure in time of simulation 
all structure were complete.


VMD is good for visualizing and some analysis, but it's not going to 
tell you anything about the physical validity of your simulation or the 
methods you used. That's what grompp was warning you about in the first 
place. If the simulation finished, there was likely no problem; the 
warning is intended to tell you that things *may* be unstable with 
Parrinello-Rahman if you are simultaneously generating velocities.



I will do your advise, and I will run with Benedsen probably it will solve my 
problem


The "broken" molecule is not a problem and will not be magically solved 
by using a different barostat.


-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] using enegygrps

[kordzadeh]

Hi all

I want to investigate interaction drug and bilayer for more detailed 
investigation I want to use energygrps for functional group of drug to find out 
which part of drug has more interaction.

is energygrps good tool?

Thank you very much

Regards

Azadeh

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Re: [gmx-users] pressure coupling error in umbrella sampling

[kordzadeh]

Hi Dr.Lemkul

Thank you very much for your answer

I get it now, before your answer I run system with -maxwarn 1, I saw trajectory 
in vmd , my drug molecule break in middle of run and then corrected, is it 
wrong?

has it occured because using maxwran?

is vmd an appropriate tool for detect trajectory?

I alaways after run, check trajectory with vmd to sure in time of simulation 
all structure were complete.

I will do your advise, and I will run with Benedsen probably it will solve my 
problem

Thank you very much

Regards

Azadeh

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Re: [gmx-users] Flexible and posres

[Justin Lemkul]

On 2/14/18 12:18 PM, Iman Ahmadabadi wrote:

Dear Mark,

I forgot the D in -DPOSRES in the previous email. However I used the
"define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
was not applied on the atoms. Is there another way to solve the problem?


What proof can you offer that the restraints did not work? What you have 
above is correct syntax and has worked in GROMACS versions dating back 
basically forever.


-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] Flexible and posres

[Iman Ahmadabadi]

Dear Mark,

I forgot the D in -DPOSRES in the previous email. However I used the
"define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
was not applied on the atoms. Is there another way to solve the problem?

Respectfully,
Iman

On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi  wrote:

> Dear Gromacs Users,
>
> If I wanna use some flexible bonds and also use position restraint on some
> other atoms, how should I do this? the error arises because 2 define =
> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>
> Respectfully
>
>
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Re: [gmx-users] Calculation of shape change of a protein during simulation

[Sudip Das]

Dear Joao and Thomas,

Thanks a lot for your kind reply. I am able to calculate the desired
properties by following your answer.

Best regards,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Feb 14, 2018 at 10:11 PM, Thomas Evangelidis 
wrote:

> You can calculate properties describing molecular shape using PLUMED as a
> trajectory post-processing tool. Example input:
>
>
> GROUP
> ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
> 22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,
> 42,43,44,45,46,47
> LABEL=al
>
> GYRATION TYPE=RADIUS ATOMS=al LABEL=rg_al
> GYRATION TYPE=TRACE ATOMS=al LABEL=tr_al
> GYRATION TYPE=GTPC_1 ATOMS=al LABEL=gtpc1_al
> GYRATION TYPE=GTPC_2 ATOMS=al LABEL=gtpc2_al
> GYRATION TYPE=GTPC_3 ATOMS=al LABEL=gtpc3_al
> GYRATION TYPE=ASPHERICITY ATOMS=al LABEL=asph_al
> GYRATION TYPE=ACYLINDRICITY ATOMS=al LABEL=acyl_al
> GYRATION TYPE=KAPPA2 ATOMS=al LABEL=K2_al
> GYRATION TYPE=RGYR_3 ATOMS=al LABEL=g3_al
> GYRATION TYPE=RGYR_2 ATOMS=al LABEL=g2_al
> GYRATION TYPE=RGYR_1 ATOMS=al LABEL=g1_al
>
> PRINT ARG=rg_al,tr_al,gtpc1_al,gtpc2_al,gtpc3_al,asph_al,
> acyl_al,K2_al,g3_al
> ,g2_al,g1_al STRIDE=1 FILE=shape_hsp90
>
>
>
>
>
>
> --
>
> ==
>
> Dr Thomas Evangelidis
>
> Post-doctoral Researcher
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/2S049,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
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>
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Re: [gmx-users] Calculation of shape change of a protein during simulation

[Thomas Evangelidis]

You can calculate properties describing molecular shape using PLUMED as a
trajectory post-processing tool. Example input:


GROUP
ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47
LABEL=al

GYRATION TYPE=RADIUS ATOMS=al LABEL=rg_al
GYRATION TYPE=TRACE ATOMS=al LABEL=tr_al
GYRATION TYPE=GTPC_1 ATOMS=al LABEL=gtpc1_al
GYRATION TYPE=GTPC_2 ATOMS=al LABEL=gtpc2_al
GYRATION TYPE=GTPC_3 ATOMS=al LABEL=gtpc3_al
GYRATION TYPE=ASPHERICITY ATOMS=al LABEL=asph_al
GYRATION TYPE=ACYLINDRICITY ATOMS=al LABEL=acyl_al
GYRATION TYPE=KAPPA2 ATOMS=al LABEL=K2_al
GYRATION TYPE=RGYR_3 ATOMS=al LABEL=g3_al
GYRATION TYPE=RGYR_2 ATOMS=al LABEL=g2_al
GYRATION TYPE=RGYR_1 ATOMS=al LABEL=g1_al

PRINT ARG=rg_al,tr_al,gtpc1_al,gtpc2_al,gtpc3_al,asph_al,acyl_al,K2_al,g3_al
,g2_al,g1_al STRIDE=1 FILE=shape_hsp90






-- 

==

Dr Thomas Evangelidis

Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

[Justin Lemkul]

On 2/14/18 9:42 AM, Justin Lemkul wrote:



On 2/14/18 9:33 AM, Easton J.W. wrote:

Thanks Justin,


Will this effect the interactions (both bonded and non-bonded) that 
these atoms have, as their atom types are not in the forcefield itp 
files?


Missing atom types would cause grompp to fail; you'd never get to the 
point where a simulation would be affected.


You're introducing custom atom types in the topology itself, and 
that's always legal before any [moleculetype] appears. The LJ 
parameters come from the [atomtypes] directive. Masses and charges 
present in that directive aren't used.




Actually, to clarify: *if* masses are present in the [atoms] directive 
of a [moleculetype], then the masses found in [atomtypes] are not used. 
Strictly speaking, it is not necessary to have explicit masses in 
[atoms], though nearly all topologies do.


-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] Potential issue using acpype to convert amber topology to gromacs

[Justin Lemkul]

On 2/14/18 9:33 AM, Easton J.W. wrote:

Thanks Justin,


Will this effect the interactions (both bonded and non-bonded) that these atoms 
have, as their atom types are not in the forcefield itp files?


Missing atom types would cause grompp to fail; you'd never get to the 
point where a simulation would be affected.


You're introducing custom atom types in the topology itself, and that's 
always legal before any [moleculetype] appears. The LJ parameters come 
from the [atomtypes] directive. Masses and charges present in that 
directive aren't used.


-Justin



Kind regards,


James


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

Sent: 14 February 2018 14:22:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 7:14 AM, Easton J.W. wrote:

Hi,


I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm 
using the amber14sb forcefield.


At the top of the top file generated, is an [atomtypes] section. Most of the 
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so 
I deleted them however there were two atomtypes A2C and A3C that were not, so I 
left them.


Looking back at my files after running some simulations I have realised that 
these were meant to be the 2C and 3C atomtypes, which had been converted. I've 
also realised that they do not have any mass in the atomtypes section.


---


[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
   A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
1.91  0.1094
   A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
1.91  0.1094

[ moleculetype ]
;namenrexcl
Peptide   3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
   1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
   2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
   3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
   4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
   5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
   6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
   7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
   8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
   9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
  10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
  11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000

---

What will this mean for the simulations that I have run?

The mass and charge information will be taken from [atoms], which always
over-writes [atomtypes] for those quantities. So there should be no
physical problem, e.g. from a "massless" atom. You can verify the masses
by using gmx dump on your .tpr file and checking that they're non-zero
for those atoms, but grompp would have failed before that point if they
were truly massless.

-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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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] Potential issue using acpype to convert amber topology to gromacs

[Easton J . W .]

Thanks Justin,


Will this effect the interactions (both bonded and non-bonded) that these atoms 
have, as their atom types are not in the forcefield itp files?


Kind regards,


James


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

Sent: 14 February 2018 14:22:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology 
to gromacs



On 2/14/18 7:14 AM, Easton J.W. wrote:
> Hi,
>
>
> I've used acpype to convert my prmtop and inpcrd files into gromacs format. 
> I'm using the amber14sb forcefield.
>
>
> At the top of the top file generated, is an [atomtypes] section. Most of the 
> atoms in this section were present in the atomtypes.atp and ffnonbonded.itp 
> so I deleted them however there were two atomtypes A2C and A3C that were not, 
> so I left them.
>
>
> Looking back at my files after running some simulations I have realised that 
> these were meant to be the 2C and 3C atomtypes, which had been converted. 
> I've also realised that they do not have any mass in the atomtypes section.
>
>
> ---
>
>
> [ atomtypes ]
> ;name   bond_type mass charge   ptype   sigma epsilon   
> Amb
>   A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
> 1.91  0.1094
>   A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
> 1.91  0.1094
>
> [ moleculetype ]
> ;namenrexcl
> Peptide   3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
> bond_type
>   1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
>   2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
>   3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
>   4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
>   5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
>   6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
>   7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
>   8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
>   9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
>  10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
>  11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000
>
> ---
>
> What will this mean for the simulations that I have run?

The mass and charge information will be taken from [atoms], which always
over-writes [atomtypes] for those quantities. So there should be no
physical problem, e.g. from a "massless" atom. You can verify the masses
by using gmx dump on your .tpr file and checking that they're non-zero
for those atoms, but grompp would have failed before that point if they
were truly massless.

-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] Potential issue using acpype to convert amber topology to gromacs

[Justin Lemkul]

On 2/14/18 7:14 AM, Easton J.W. wrote:

Hi,


I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm 
using the amber14sb forcefield.


At the top of the top file generated, is an [atomtypes] section. Most of the 
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so 
I deleted them however there were two atomtypes A2C and A3C that were not, so I 
left them.


Looking back at my files after running some simulations I have realised that 
these were meant to be the 2C and 3C atomtypes, which had been converted. I've 
also realised that they do not have any mass in the atomtypes section.


---


[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
  A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
1.91  0.1094
  A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 
1.91  0.1094

[ moleculetype ]
;namenrexcl
Peptide   3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
  1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
  2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
  3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
  4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
  5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
  6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
  7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
  8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
  9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
 10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
 11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000

---

What will this mean for the simulations that I have run?


The mass and charge information will be taken from [atoms], which always 
over-writes [atomtypes] for those quantities. So there should be no 
physical problem, e.g. from a "massless" atom. You can verify the masses 
by using gmx dump on your .tpr file and checking that they're non-zero 
for those atoms, but grompp would have failed before that point if they 
were truly massless.


-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] Rupture force definition

[Justin Lemkul]

On 2/14/18 7:31 AM, Rakesh Mishra wrote:

Dear Justin,

Can you explain something regarding this issue.

I couldn't get  resolve one  problem.  Though now I am able to make
restrict (immobile )
the needed residue and pulled another one.
But the contradiction that i am facing is that, when I am pulling with
-rate (in negative z direction, as I want to pull
the residue in the negative Z direction of box ) given below.
Still there we see  that pulling group is not moving the -ve direction of
z.


Your settings are right, so either you need a larger force constant to 
induce the motion or you need to wait longer for the restoring forces in 
the system (whatever they are) to be overcome by the biasing potential.


-Justin



pull   = yes
pull_ngroups  = 2
pull_ncoords  = 1
pull_group1_name  = chain-A-start
pull_group2_name  = chain-B-end
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= -0.01  ;  0.01 nm per ps = 10 per 1 ns
pull_coord1_k= 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance >
0


Best



On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra  wrote:


Thank you very much Justin.

Here it is working but having some  problem.
pull_group2_name = chain_B35  is moving in the + z direction &
pull_group4_name= chain_B26   is  moving oppositely in the -z direction
While I have given pull in +z direction for both the above group.

Note - pull_group1_name = chain_A8 and  pull_group3_name  = chain_A17 are
immobile here as well as acting as reference.


On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul  wrote:



On 2/1/18 7:59 AM, Rakesh Mishra wrote:


Dear Justin

Here I am applying pull for two groups with respect to two reference
group
as following.
; Pull code
pull= yes
pull_ngroups= 4
pull_ncoords= 1
pull_group1_name= chain_A8 (reference  also immobile )
pull_group2_name= chain_B35   (pulling group)
pull_group3_name= chain_A17(reference also immobile)
pull_group4_name= chain_B26(pulling)
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per 1 ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0

In above protocol I want to make two reference group  as
1-chain_A8   2- chain_A17
and two pull group.
1- chain_B35  2- chain_B26


You've defined four groups but then only used two, so you only get the
effect of one reaction coordinate.

What you need to do is define the pull settings for all reaction
coordinates simultaneously, e.g.:

pull= yes
pull_ngroups= 4
pull_ncoords= 2
pull_group1_name= chain_A8
pull_group2_name= chain_B35
pull_group3_name= chain_A17
pull_group4_name= chain_B26
; definition of reaction coordinate 1, groups 1-2
pull_coord1_type= umbrella
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01
pull_coord1_k   = 1000
pull_coord1_start   = yes
; definition of reaction coordinate 2, groups 3-4
pull_coord2_type= umbrella
pull_coord2_geometry= distance
pull_coord2_groups  = 3 4
pull_coord2_dim = N N Y
pull_coord2_rate= 0.01
pull_coord2_k   = 1000
pull_coord2_start   = yes

Note that above I changed pull_ncoords to be set to 2, because you want
two reaction coordinates. Then just specify the settings for each one,
calling the appropriate groups by their assigned 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.biochem.vt.edu/people/faculty/JustinLemkul.html

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--
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491 <094736%2062491>, +91877749632*






--

Re: [gmx-users] Flexible and posres

[Mark Abraham]

Hi,

Please copy and paste your attempts and the errors, if you want to get
effectively help. You can use

define = -DPOSRES -DFLEXIBLE

to combine them, and -POSRES is always wrong.

Mark

On Wed, Feb 14, 2018 at 3:19 PM Iman Ahmadabadi 
wrote:

> Dear Gromacs Users,
>
> If I wanna use some flexible bonds and also use position restraint on some
> other atoms, how should I do this? the error arises because 2 define =
> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>
> Respectfully
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] the energy of the individual molecule

[Justin Lemkul]

On 2/13/18 11:48 AM, dgfd dgdfg wrote:

Suppose the trajectory of molecular system with interactions between all 
molecules. How is to obtain the time dependence of intramolecular energy of the 
given molecule with unique resname and the total energy of this molecule in the 
system including intermolecular interactions?


Save the subset of coordinates that you care about from the trajectory 
with trjconv, make a matching subset .tpr with convert-tpr, and use 
mdrun-rerun.


The values you get may not have any physical meaning, depending on how 
the force field was parametrized.


-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] Flexible and posres

[Iman Ahmadabadi]

Dear Gromacs Users,

If I wanna use some flexible bonds and also use position restraint on some
other atoms, how should I do this? the error arises because 2 define =
-DFLEXIBLE and -POSRES is not allowed in the .mdp files.

Respectfully
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Re: [gmx-users] Pulling protein from distance on membrane

[Justin Lemkul]

On 2/13/18 5:24 AM, Souparno Adhikary wrote:

Hi,

I am trying to simulate a system in which a protein will be pulled from a
distance and ultimately be put on a DPPC membrane system. I went through
Lemkul's tutorial on membrane and successfully simulated protein-membrane
systems before.

In this case, I put the protein in the required coordinates using editconf
(distant from the membrane). Whenever I'm running the inflategro script
(provided by Justin Lemkul in his webpage), the system breaks apart
(specifically the protein).

Please give me an idea how can I put the protein outside the membrane and
then pull it on the membrane.


If the protein is outside the membrane, why are you running InflateGRO? 
That's only for packing lipids around an embedded membrane.


Define a proper box, position the components in it, solvate and add 
ions, and proceed. There's no need for extra work.


-Justin


To say about the protein, it is not usually considered a membrane
interacting protein. Some recent publications highlighted the activity of
the protein as it pulls away some of the membrane lipids after interacting.
Earlier, when I've simulated the protein in the membrane and put some weak
force on the protein to make it go away from the membrane, I have
successfully found the experimental results. Now, I want to put the protein
from outside the membrane (as the phenomenon takes place in the in vitro
system).

Thanks in advance,


Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.


--
==

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] GROMOS96 53A6 with extended Berger lipid parameters (Prasanna)

[Justin Lemkul]

On 2/13/18 5:08 AM, Prasanna Dr wrote:

Hi all,

The force field combination used in GROMOS96 53A6 with extended Berger
lipids contains L-J interaction cross-terms between protein lipid atom
types? If so how abnormally high L-J interactions are tackled?

In my case, to prepare the topology of my system (which contains proteins
and DPPC), I followed KALP15 in DPPC tutorial (version Gromacs 5.0 and
above) of Justin A. Lemkul.  Does this tutorial answers my first question?
Does I have employed force filed combination rules effectively?


Force field combination rules are only overridden when using a 
[nonbond_params] directive. If you find something abnormal that needs to 
be fixed, then you'd implement it there. Note that the tutorial is 
instructive in demonstrating how to set up such a system, but it is not 
the best possible force field model out there.


-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] charmm36 force field

[Justin Lemkul]

On 2/12/18 3:09 PM, farial tavakoli wrote:

First, please note that this line is not doing anything:

define        =  -DUSE_OLD_C3


If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, 
the correct keyword is -DUSE_OLD_C36. We only included that in the case 
that people wanted to do force field comparisons, because for folded 
proteins, C36 and C36m are almost identical by virtue of how we did the 
reparametrization.



but when I checked nvt.gro by VMD ,  viewed  the receptor and ligand went out 
of the box, almost completely and ligand was separated from the protein, 
completely. Is there anyone who can help me and advice me why it was happened?


Sounds like a typical PBC imaging issue. Just use trjconv.

-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] how can i restrain Zn ion during simulations

[Justin Lemkul]

On 2/12/18 10:29 AM, vijayakumar gosu wrote:

Dear gromacs users,


I am currently running simulations for protein-RNA complex. However i have
to include one Zn ion which is coordinated by 4 cysteine residues. when i
performed energy minimization itself zinc displaces. How can i restrain to
Zn, or to freeze Zn during simulations.


Are you properly treating the Cys residues as anionic? If they're in the 
normal -SH state, I'd expect such a dissociation, but if they carry a -1 
charge (as expected when coordinating Zn2+), I find that rather unusual.


You can enforce the coordination geometry with bonds, harmonic 
connections, or distance restraints. Check the manual for explanations.


-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] PBC

[Justin Lemkul]

On 2/12/18 8:44 AM, Ahmed Mashaly wrote:

Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference 
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the 
first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use 
md.tpr as reference for md.xtc, I will have to recenter it after every step of 
em, nvt, npt


You can use whatever reference coordinates you want. Energy minimization 
generally shouldn't result in large structural changes, so make sure you 
have a sufficiently large box to avoid spurious minimum image interactions.


-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] pressure coupling error in umbrella sampling

[Justin Lemkul]

On 2/12/18 6:34 AM, kordza...@aut.ac.ir wrote:

Hi Dr.Abraham

Thank you very much for your answer

yas I ve extacted configuration with 0.2 nm distance and when I want to 
run NPT for first configuration,I gave that error.

I didnt undersatnd this mdp file for this step, I got this file from umbrella 
sampling tutorial and I adjusted for my system but I didnt understand

we are doing a pullind simulation with zero velocity, I think the aim is to 
costriant structure by artifial spring but we dont  move it, am I right?


The application of a biasing potential (which is not a constraint) is 
separate from the technical issue of Parrinello-Rahman pressure coupling 
being applied in conjunction with generating velocities. I wrote the 
tutorial and input files years ago when grompp didn't complain about 
this. I had no problems with stability, but this may not always be the 
case. So grompp is trying to help you by pointing out that this 
particular combination of options may not be wise. You may wish to do a 
short NPT equilibration with Berendsen pressure coupling before starting 
data collection.


-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] Rupture force definition

[Rakesh Mishra]

Dear Justin,

Can you explain something regarding this issue.

I couldn't get  resolve one  problem.  Though now I am able to make
restrict (immobile )
the needed residue and pulled another one.
But the contradiction that i am facing is that, when I am pulling with
-rate (in negative z direction, as I want to pull
the residue in the negative Z direction of box ) given below.
Still there we see  that pulling group is not moving the -ve direction of
z.


pull   = yes
pull_ngroups  = 2
pull_ncoords  = 1
pull_group1_name  = chain-A-start
pull_group2_name  = chain-B-end
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= -0.01  ;  0.01 nm per ps = 10 per 1 ns
pull_coord1_k= 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance >
0


Best



On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra  wrote:

> Thank you very much Justin.
>
> Here it is working but having some  problem.
> pull_group2_name = chain_B35  is moving in the + z direction &
> pull_group4_name= chain_B26   is  moving oppositely in the -z direction
> While I have given pull in +z direction for both the above group.
>
> Note - pull_group1_name = chain_A8 and  pull_group3_name  = chain_A17 are
> immobile here as well as acting as reference.
>
>
> On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 2/1/18 7:59 AM, Rakesh Mishra wrote:
>>
>>> Dear Justin
>>>
>>> Here I am applying pull for two groups with respect to two reference
>>> group
>>> as following.
>>> ; Pull code
>>> pull= yes
>>> pull_ngroups= 4
>>> pull_ncoords= 1
>>> pull_group1_name= chain_A8 (reference  also immobile )
>>> pull_group2_name= chain_B35   (pulling group)
>>> pull_group3_name= chain_A17(reference also immobile)
>>> pull_group4_name= chain_B26(pulling)
>>> pull_coord1_type= umbrella  ; harmonic biasing force
>>> pull_coord1_geometry= distance  ; simple distance increase
>>> pull_coord1_groups  = 1 2
>>> pull_coord1_dim = N N Y
>>> pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per 1 ns
>>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
>>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>>
>>> In above protocol I want to make two reference group  as
>>> 1-chain_A8   2- chain_A17
>>> and two pull group.
>>> 1- chain_B35  2- chain_B26
>>>
>>
>> You've defined four groups but then only used two, so you only get the
>> effect of one reaction coordinate.
>>
>> What you need to do is define the pull settings for all reaction
>> coordinates simultaneously, e.g.:
>>
>> pull= yes
>> pull_ngroups= 4
>> pull_ncoords= 2
>> pull_group1_name= chain_A8
>> pull_group2_name= chain_B35
>> pull_group3_name= chain_A17
>> pull_group4_name= chain_B26
>> ; definition of reaction coordinate 1, groups 1-2
>> pull_coord1_type= umbrella
>> pull_coord1_geometry= distance
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.01
>> pull_coord1_k   = 1000
>> pull_coord1_start   = yes
>> ; definition of reaction coordinate 2, groups 3-4
>> pull_coord2_type= umbrella
>> pull_coord2_geometry= distance
>> pull_coord2_groups  = 3 4
>> pull_coord2_dim = N N Y
>> pull_coord2_rate= 0.01
>> pull_coord2_k   = 1000
>> pull_coord2_start   = yes
>>
>> Note that above I changed pull_ncoords to be set to 2, because you want
>> two reaction coordinates. Then just specify the settings for each one,
>> calling the appropriate groups by their assigned 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.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
>> 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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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> * Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 

[gmx-users] Potential issue using acpype to convert amber topology to gromacs

[Easton J . W .]

Hi,


I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm 
using the amber14sb forcefield.


At the top of the top file generated, is an [atomtypes] section. Most of the 
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so 
I deleted them however there were two atomtypes A2C and A3C that were not, so I 
left them.


Looking back at my files after running some simulations I have realised that 
these were meant to be the 2C and 3C atomtypes, which had been converted. I've 
also realised that they do not have any mass in the atomtypes section.


---


[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 A2C  A2C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 A3C  A3C 0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094

[ moleculetype ]
;namenrexcl
Peptide   3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1N 1   CYS N1-0.415700 14.01000 ; qtot -0.416
 2H 1   CYS H2 0.271900  1.00800 ; qtot -0.144
 3   CX 1   CYSCA3 0.021300 12.01000 ; qtot -0.123
 4   H1 1   CYSHA4 0.112400  1.00800 ; qtot -0.010
 5  A2C 1   CYSCB5-0.123100 12.01000 ; qtot -0.133
 6   H1 1   CYS   HB26 0.111200  1.00800 ; qtot -0.022
 7   H1 1   CYS   HB37 0.111200  1.00800 ; qtot 0.089
 8   SH 1   CYSSG8-0.311900 32.06000 ; qtot -0.223
 9   HS 1   CYSHG9 0.193300  1.00800 ; qtot -0.029
10C 1   CYS C   10 0.597301 12.01000 ; qtot 0.568
11O 1   CYS O   11-0.567901 16.0 ; qtot -0.000

---

What will this mean for the simulations that I have run?


Kind regards,


James
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[gmx-users] printing neighbor list

[fabio trovato]

Hi,

I am trying to output the neighbor list calculated during a simulation. I
consulted the manual which says that DUMPNL is the env variable suited for
this purpose.

In my bash script I first set up:
export DUMPNL=10

and then run the simulation (GROMACS version 4.5.4).

I do not see any neighbor list printed in my md.log file. What am I doing
wrong? Does anyone knows how to solve this?

Thank you,
Fabio
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