Re: [gmx-users] gmx hbond

[rose rahmani]

Thank you. But it just adjusts the cut-off between atoms not the number of
hydrogen bonds in a given distance above the surface (or in the box). would
you please help me?

Best

On Sun, Jan 6, 2019 at 9:12 PM paul buscemi  wrote:

> Use VMD/extensions/hydrogen bonds
>
> > On Jan 6, 2019, at 11:01 AM, rose rahmani  wrote:
> >
> > hi,
> >
> > I want to know the number of hydrogen bonds of amino acid with water in
> > different distances above surface. for example in first 0.2nm, in second
> > 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I
> couldn't
> > find any proper option for that.
> >
> > best
> > --
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[gmx-users] gmx hbond

[rose rahmani]

hi,

I want to know the number of hydrogen bonds of amino acid with water in
different distances above surface. for example in first 0.2nm, in second
0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't
find any proper option for that.

best
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Re: [gmx-users] how to calculated potential energy ?

[rose rahmani]

But CHARMM ff can calculate intermolecular interaction energy which
contributed to enthalpy, yes?

On Fri, 4 Jan 2019, 11:27 Mark Abraham  Hi,
>
> You can use trjconv and tpbconv to make matching subsets of the trajectory
> and tpr files, and then mdrun -rerun will compute the contributions on
> those subsets. But I doubt there's force fields where any of this is
> meaningful.
>
> Mark
>
> On Tue, Jan 1, 2019 at 1:47 PM milad bagheri 
> wrote:
>
> > Dear researcher
> > I want to measure the following parameters for a part of a protein
> >
> > Intramolecular potential energy
> >
> > protein surface potential
> >
> > Ebond, bond length potential energy contribution
> >
> > Eangle, bond angle potential energy contribution
> >
> > Etorsion, torsion angle potential energy contribution
> >
> > Eelectro, electrostatic potential energy contribution
> >
> > EvdW, Van der Waals potential energy contribution
> > How to do this with gromacs?
> > --
> > Gromacs Users mailing list
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> > posting!
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> >
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Re: [gmx-users] Interaction energy

[rose rahmani]

How can i find these information about charmm forcefield? Would you please
help me?

On Tue, 27 Nov 2018, 00:22 Mark Abraham  Hi,
>
> On Mon, Nov 26, 2018 at 7:47 PM Nick Johans 
> wrote:
>
> > On Mon, 26 Nov 2018, 21:28 Justin Lemkul  >
> > >
> > >
> > > On 11/26/18 10:51 AM, Nick Johans wrote:
> > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  > > >
> > > >>
> > > >> On 11/22/18 11:41 AM, Nick Johans wrote:
> > > >>> Hi
> > > >>>
> > > >>> I am beginner in MD. Maybe it is not a wise question but i want to
> > > >>> calculate the interaction energy between protein and ligand and
> also
> > > PMF
> > > >> in
> > > >>> different distances. But i don't know what is the didference
> between
> > > >> PMF, i
> > > >>> mean free energy in particular(by umbrella sampling) and the
> > > interaction
> > > >>> energy (by g_energy tool) in my case?
> > > >> Interaction energy is a pairwise decomposition of short-range
> > nonbonded
> > > >> interaction energy in the system. This energy is usually not
> > physically
> > > >> meaningful, but if the force field has been parametrized in such a
> way
> > > >> that it is, the interaction energy is a contribution to the enthalpy
> > of
> > > >> the system.
> > > >>
> > > > What forcefields embedded in GROMACS do, yes?
> > >
> > > AFAIK only CHARMM.
> > >
> > Interesting! You mean interaction energy calculated by for example AMBER
> > may not be true? Why?? What makes CHARMM unique??
> >
>
> As Justin said, the difference is in the way it is parametrized.
> Forcefields are generally built to be additive, but it does not follow that
> they are decomposable.
>
> > > If coulomb energy is also existed between pairs, so the interaction
> > > energy
> > > > will be LJ+Coulomb yes?
> > >
> > > Pairs are 1-4 (intramolecular) interactions, so if you define
> > > interaction energy between two nonbonded species, you'll get zeroes for
> > > all the pair energies, by definition.
> > >
> > It's exactly the SR(short range) selection in g_energy, yes?
>
>
> You seem to be using a looser definition of pairs than is usual in
> discussion of GROMACS topologies.
>
>
> > all long range
> > are zero.
>
>
> If there's a long-range model, then such interactions are not uniformly of
> zero magnitude...
>
>
> > But coulomb and LJ are non-zero. So, in this case the interaction
> > energy would be
> > Short range LJ+ Short range Coulomb , true?
> >
>
> As far as I'm concerned, you can invent whatever quantity you want, but the
> burden is on you to demonstrate that there's a reason to connect it to
> something physical.
>
> Mark
>
>
> > >
> > > > So what about PMF. It seems like an interaction energy too, but more
> > > > accurate one???
> > >
> > > That's not what a PMF is. A PMF is the change in free energy of a
> system
> > > as a function of progress along a reaction coordinate.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Office: 301 Fralin Hall
> > > Lab: 303 Engel Hall
> > >
> > > Virginia Tech Department of Biochemistry
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.thelemkullab.com
> > >
> > > ==
> > >
> > > --
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> > >
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Re: [gmx-users] Gmx mindist

[rose rahmani]

Also i have used this command

G_mindist -f md2.gro -s -n -or (select Pr-H and tube)

Dies it calculate minimum distabce of non-hydrogen atom of each residue
with tube closest atom or COM of nanotube?

On Mon, 31 Dec 2018, 03:03 rose rahmani  Hi,
>
> Does g_mindist calculates distances between COM of two groups?
>
> I want twi calculate dustances between any atom of protein-H and nanotube
> surface. So if g_mindist shows for example 0.9nm is it really 0.9-0.7(tube
> radius)=0.2 nm from surface?
>
> Best
>
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[gmx-users] Gmx mindist

[rose rahmani]

Hi,

Does g_mindist calculates distances between COM of two groups?

I want twi calculate dustances between any atom of protein-H and nanotube
surface. So if g_mindist shows for example 0.9nm is it really 0.9-0.7(tube
radius)=0.2 nm from surface?

Best
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Re: [gmx-users] Gmx gangle

[rose rahmani]

Would you please answer my question? Did you check it?

On Wed, 12 Dec 2018, 02:03 Mark Abraham  Hi,
>
> I would check the documentation of gmx gangle for how it works,
> particularly for how to define a plane. Also, 4.5.4 is prehistoric, please
> do yourself a favor and use a version with the seven years of improvements
> since then :-)
>
> Mark
>
> On Tue., 11 Dec. 2018, 10:14 rose rahmani,  wrote:
>
> > Hi,
> >
> > I don't really understand how gmx gangke works!!!
> >
> > I want to calculate angle between amino acid ring and surface during
> > simulation.
> >  I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two
> atoms
> > of surface. Surface is in xy plane and amino acid is in different Z
> > distances.
> >
> >
> > I assumed 6 ring atoms are defining a pkane and two atoms of surface are
> > defining a vector( along  Y). And i expected that the Average angle
> between
> > this plane and vector during simulation is calculated by gmx gangle
> > analysis.
> >
> >  gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav
> > angz.xvg -g1 plane -g2 vector -group1 -group2
> >
> > Available static index groups:
> >  Group  0 "System" (4331 atoms)
> >  Group  1 "Other" (760 atoms)
> >  Group  2 "ZnS" (560 atoms)
> >  Group  3 "WAL" (200 atoms)
> >  Group  4 "NA" (5 atoms)
> >  Group  5 "CL" (5 atoms)
> >  Group  6 "Protein" (33 atoms)
> >  Group  7 "Protein-H" (17 atoms)
> >  Group  8 "C-alpha" (1 atoms)
> >  Group  9 "Backbone" (5 atoms)
> >  Group 10 "MainChain" (7 atoms)
> >  Group 11 "MainChain+Cb" (8 atoms)
> >  Group 12 "MainChain+H" (9 atoms)
> >  Group 13 "SideChain" (24 atoms)
> >  Group 14 "SideChain-H" (10 atoms)
> >  Group 15 "Prot-Masses" (33 atoms)
> >  Group 16 "non-Protein" (4298 atoms)
> >  Group 17 "Water" (3528 atoms)
> >  Group 18 "SOL" (3528 atoms)
> >  Group 19 "non-Water" (803 atoms)
> >  Group 20 "Ion" (10 atoms)
> >  Group 21 "ZnS" (560 atoms)
> >  Group 22 "WAL" (200 atoms)
> >  Group 23 "NA" (5 atoms)
> >  Group 24 "CL" (5 atoms)
> >  Group 25 "Water_and_ions" (3538 atoms)
> >  Group 26 "OW" (1176 atoms)
> >  Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
> >  Group 28 "a_320_302_319_301_318_311" (6 atoms)
> >  Group 29 "a_301_302" (2 atoms)
> > Specify any number of selections for option 'group1'
> > (First analysis/vector selection):
> > (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > > 27
> > Selection '27' parsed
> > > 27
> > Selection '27' parsed
> > > Available static index groups:
> >  Group  0 "System" (4331 atoms)
> >  Group  1 "Other" (760 atoms)
> >  Group  2 "ZnS" (560 atoms)
> >  Group  3 "WAL" (200 atoms)
> >  Group  4 "NA" (5 atoms)
> >  Group  5 "CL" (5 atoms)
> >  Group  6 "Protein" (33 atoms)
> >  Group  7 "Protein-H" (17 atoms)
> >  Group  8 "C-alpha" (1 atoms)
> >  Group  9 "Backbone" (5 atoms)
> >  Group 10 "MainChain" (7 atoms)
> >  Group 11 "MainChain+Cb" (8 atoms)
> >  Group 12 "MainChain+H" (9 atoms)
> >  Group 13 "SideChain" (24 atoms)
> >  Group 14 "SideChain-H" (10 atoms)
> >  Group 15 "Prot-Masses" (33 atoms)
> >  Group 16 "non-Protein" (4298 atoms)
> >  Group 17 "Water" (3528 atoms)
> >  Group 18 "SOL" (3528 atoms)
> >  Group 19 "non-Water" (803 atoms)
> >  Group 20 "Ion" (10 atoms)
> >  Group 21 "ZnS" (560 atoms)
> >  Group 22 "WAL" (200 atoms)
> >  Group 23 "NA" (5 atoms)
> >  Group 24 "CL" (5 atoms)
> >  Group 25 "Water_and_ions" (3538 atoms)
> >  Group 26 "OW" (1176 atoms)
> >  Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
> >  Group 28 "a_320_302_319_301_318_311" (6 atoms)
> >  Group 29 "a_301_302" (2 atoms)
> > Specify any number of selections for option 'group2'
> > (Second analysis/vector selection):
> > (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > > 29
> > Selection '29' parsed
> > >

Re: [gmx-users] Gmx gangle

[rose rahmani]

On Wed, 12 Dec 2018, 02:03 Mark Abraham  Hi,
>
> I would check the documentation of gmx gangle for how it works,
> particularly for how to define a plane.

Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I
think sth it would be REALLY helpful if you provide some proper examples
for gromacs tools, with results. You have straightforward tutorials and
useful manual, but some instructions in using tools, are a little ambiguous
and misleading. This also reduces the number of questions.

> Also, 4.5.4 is prehistoric, please
> do yourself a favor

I would like, but I remember that I wanted to use cutoff-scheme=group and i
couldnt come up with errors in gmx. These calculations are for more than
one year ago (and now I want some more analysis), i was a freshman,

> and use a version with the seven years of improvements
>
I was a freshman,  dear smiling man -:)

> since then :-)
>
I am waiting for you.

Best

>
> Mark
>
> On Tue., 11 Dec. 2018, 10:14 rose rahmani,  wrote:
>
> > Hi,
> >
> > I don't really understand how gmx gangke works!!!
> >
> > I want to calculate angle between amino acid ring and surface during
> > simulation.
> >  I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two
> atoms
> > of surface. Surface is in xy plane and amino acid is in different Z
> > distances.
> >
> >
> > I assumed 6 ring atoms are defining a pkane and two atoms of surface are
> > defining a vector( along  Y). And i expected that the Average angle
> between
> > this plane and vector during simulation is calculated by gmx gangle
> > analysis.
> >
> >  gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav
> > angz.xvg -g1 plane -g2 vector -group1 -group2
> >
> > Available static index groups:
> >  Group  0 "System" (4331 atoms)
> >  Group  1 "Other" (760 atoms)
> >  Group  2 "ZnS" (560 atoms)
> >  Group  3 "WAL" (200 atoms)
> >  Group  4 "NA" (5 atoms)
> >  Group  5 "CL" (5 atoms)
> >  Group  6 "Protein" (33 atoms)
> >  Group  7 "Protein-H" (17 atoms)
> >  Group  8 "C-alpha" (1 atoms)
> >  Group  9 "Backbone" (5 atoms)
> >  Group 10 "MainChain" (7 atoms)
> >  Group 11 "MainChain+Cb" (8 atoms)
> >  Group 12 "MainChain+H" (9 atoms)
> >  Group 13 "SideChain" (24 atoms)
> >  Group 14 "SideChain-H" (10 atoms)
> >  Group 15 "Prot-Masses" (33 atoms)
> >  Group 16 "non-Protein" (4298 atoms)
> >  Group 17 "Water" (3528 atoms)
> >  Group 18 "SOL" (3528 atoms)
> >  Group 19 "non-Water" (803 atoms)
> >  Group 20 "Ion" (10 atoms)
> >  Group 21 "ZnS" (560 atoms)
> >  Group 22 "WAL" (200 atoms)
> >  Group 23 "NA" (5 atoms)
> >  Group 24 "CL" (5 atoms)
> >  Group 25 "Water_and_ions" (3538 atoms)
> >  Group 26 "OW" (1176 atoms)
> >  Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
> >  Group 28 "a_320_302_319_301_318_311" (6 atoms)
> >  Group 29 "a_301_302" (2 atoms)
> > Specify any number of selections for option 'group1'
> > (First analysis/vector selection):
> > (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> > > 27
> > Selection '27' parsed
> > > 27
> > Selection '27' parsed
> > > Available static index groups:
> >  Group  0 "System" (4331 atoms)
> >  Group  1 "Other" (760 atoms)
> >  Group  2 "ZnS" (560 atoms)
> >  Group  3 "WAL" (200 atoms)
> >  Group  4 "NA" (5 atoms)
> >  Group  5 "CL" (5 atoms)
> >  Group  6 "Protein" (33 atoms)
> >  Group  7 "Protein-H" (17 atoms)
> >  Group  8 "C-alpha" (1 atoms)
> >  Group  9 "Backbone" (5 atoms)
> >  Group 10 "MainChain" (7 atoms)
> >  Group 11 "MainChain+Cb" (8 atoms)
> >  Group 12 "MainChain+H" (9 atoms)
> >  Group 13 "SideChain" (24 atoms)
> >  Group 14 "SideChain-H" (10 atoms)
> >  Group 15 "Prot-Masses" (33 atoms)
> >  Group 16 "non-Protein" (4298 atoms)
> >  Group 17 "Water" (3528 atoms)
> >  Group 18 "SOL" (3528 atoms)
> >  Group 19 "non-Water" (803 atoms)
> >  Group 20 "Ion" (10 atoms)
> >  Group 21 "ZnS" (560 atoms)
> >  Group 22 "WAL" (200 atoms)
> >  Group 23

[gmx-users] Gmx gangle

[rose rahmani]

Hi,

I don't really understand how gmx gangke works!!!

I want to calculate angle between amino acid ring and surface during
simulation.
 I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two atoms
of surface. Surface is in xy plane and amino acid is in different Z
distances.


I assumed 6 ring atoms are defining a pkane and two atoms of surface are
defining a vector( along  Y). And i expected that the Average angle between
this plane and vector during simulation is calculated by gmx gangle
analysis.

 gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav
angz.xvg -g1 plane -g2 vector -group1 -group2

Available static index groups:
 Group  0 "System" (4331 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (33 atoms)
 Group  7 "Protein-H" (17 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (24 atoms)
 Group 14 "SideChain-H" (10 atoms)
 Group 15 "Prot-Masses" (33 atoms)
 Group 16 "non-Protein" (4298 atoms)
 Group 17 "Water" (3528 atoms)
 Group 18 "SOL" (3528 atoms)
 Group 19 "non-Water" (803 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3538 atoms)
 Group 26 "OW" (1176 atoms)
 Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
 Group 28 "a_320_302_319_301_318_311" (6 atoms)
 Group 29 "a_301_302" (2 atoms)
Specify any number of selections for option 'group1'
(First analysis/vector selection):
(one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> 27
Selection '27' parsed
> 27
Selection '27' parsed
> Available static index groups:
 Group  0 "System" (4331 atoms)
 Group  1 "Other" (760 atoms)
 Group  2 "ZnS" (560 atoms)
 Group  3 "WAL" (200 atoms)
 Group  4 "NA" (5 atoms)
 Group  5 "CL" (5 atoms)
 Group  6 "Protein" (33 atoms)
 Group  7 "Protein-H" (17 atoms)
 Group  8 "C-alpha" (1 atoms)
 Group  9 "Backbone" (5 atoms)
 Group 10 "MainChain" (7 atoms)
 Group 11 "MainChain+Cb" (8 atoms)
 Group 12 "MainChain+H" (9 atoms)
 Group 13 "SideChain" (24 atoms)
 Group 14 "SideChain-H" (10 atoms)
 Group 15 "Prot-Masses" (33 atoms)
 Group 16 "non-Protein" (4298 atoms)
 Group 17 "Water" (3528 atoms)
 Group 18 "SOL" (3528 atoms)
 Group 19 "non-Water" (803 atoms)
 Group 20 "Ion" (10 atoms)
 Group 21 "ZnS" (560 atoms)
 Group 22 "WAL" (200 atoms)
 Group 23 "NA" (5 atoms)
 Group 24 "CL" (5 atoms)
 Group 25 "Water_and_ions" (3538 atoms)
 Group 26 "OW" (1176 atoms)
 Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms)
 Group 28 "a_320_302_319_301_318_311" (6 atoms)
 Group 29 "a_301_302" (2 atoms)
Specify any number of selections for option 'group2'
(Second analysis/vector selection):
(one per line,  for status/groups, 'help' for help, Ctrl-D to end)
> 29
Selection '29' parsed
> 29
Selection '29' parsed
> Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision)
Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision)
Reading frame   0 time0.000
Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
Last frame  4 time 4000.Ö00
Analyzed 40001 frames, last ti߸ 4000.000

Am I right? I don't think so. :(

Would you please help me?
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[gmx-users] -selrpos option

[rose rahmani]

Hi,

What is the usage of -selrpos option in gmx distance,sasa,... . I don't
understand how can i use it? What is difference between mol_cog and
mol_com,...? If i wanted to calculate distance from the surface of nanotube
how can i specify it?
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[gmx-users] Gmx sasa

[rose rahmani]

Hi,

My system contains, nanotube with amino acids in aqueous solution. I want
to know how amino amicds cover nanotube surface after adsorption. Can i do
it by gmx sasa? It seems this tool just calculate (solution relavent
properties)coverage?

Best
Rose
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Re: [gmx-users] Distance calculation

[rose rahmani]

On Tue, Nov 27, 2018 at 9:23 PM Justin Lemkul  wrote:

>
>
> On 11/27/18 12:37 PM, rose rahmani wrote:
> > Great! Non-hydrogen is generally for all AAs, but i want non-hydrogen
> atoms
> > of each AA number 1, 2, 3 to be representative of one adsorption.
> Moreover,
> > if 4 non-hydrogen atoms of AA were in <0.5 nm, this should be considered
> as
> > one adsorption not 4!  How should i come up with these challenges?
>
> Your criteria need to be based on either (1) a minimum distance of any
> atom that satisfies a cutoff or (2) the COM of a group of atoms.
>
> You can easily create index groups for any residue, side chain, etc.
> that you want to consider.
>
> > And as i'm not much skilled in programming, is there any useful examples
> > for implementing python or perl in GROMACS?
>
> You don't implement Python or Perl in GROMACS. These are programming
> languages of their own. I suggest them because they are very easy to use
> for parsing text files, which is precisely what GROMACS gives you.
>
Sure, i do my best. thank you.

>
> Learn to code. It's an essential skill in this field.
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
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> http://www.thelemkullab.com
>
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Re: [gmx-users] Distance calculation

[rose rahmani]

Great! Non-hydrogen is generally for all AAs, but i want non-hydrogen atoms
of each AA number 1, 2, 3 to be representative of one adsorption. Moreover,
if 4 non-hydrogen atoms of AA were in <0.5 nm, this should be considered as
one adsorption not 4!  How should i come up with these challenges?
And as i'm not much skilled in programming, is there any useful examples
for implementing python or perl in GROMACS?

Best



On Tue, Nov 27, 2018 at 5:21 PM Justin Lemkul  wrote:

>
>
> On 11/26/18 1:59 PM, rose rahmani wrote:
> > Can i use -dist option?
> > Would you please help me?
>
> The -dist option just prints a list of atoms that satisfy the criterion;
> that's not necessarily useful to you.
>
> Use gmx mindist with appropriate selections to get the time series of
> the minimum distance of relevant non-H atoms and your nanotube. Then
> write a simple script that reports some useful quantity, like the first
> time at which the distance criterion was met or the percentage of time
> the distance was below 0.5 nm. This is trivial with something like
> Python or Perl.
>
> -Justin
>
> > On Mon, 26 Nov 2018, 00:48 rose rahmani  >
> >> Hi,
> >>
> >> My system contains 20 amino acids around nanotube. I want to know the
> >> adsorption amount of AA during simulation time; the adsorption occurs
> >> when the distance between one of non-hydrogen atoms of AA and the tube
> >> surface was less than 0.5 nm. So how can i calculate this property?
> >>
> >> Would you please help me?
> >> Best
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Distance calculation

[rose rahmani]

Can i use -dist option?
Would you please help me?
On Mon, 26 Nov 2018, 00:48 rose rahmani  Hi,
>
> My system contains 20 amino acids around nanotube. I want to know the
> adsorption amount of AA during simulation time; the adsorption occurs
> when the distance between one of non-hydrogen atoms of AA and the tube
> surface was less than 0.5 nm. So how can i calculate this property?
>
> Would you please help me?
> Best
>
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Re: [gmx-users] Interaction energy

[rose rahmani]

On Mon, 26 Nov 2018, 21:28 Justin Lemkul 
>
> On 11/26/18 10:51 AM, Nick Johans wrote:
> > On Mon, 26 Nov 2018, 18:22 Justin Lemkul  >
> >>
> >> On 11/22/18 11:41 AM, Nick Johans wrote:
> >>> Hi
> >>>
> >>> I am beginner in MD. Maybe it is not a wise question but i want to
> >>> calculate the interaction energy between protein and ligand and also
> PMF
> >> in
> >>> different distances. But i don't know what is the didference between
> >> PMF, i
> >>> mean free energy in particular(by umbrella sampling) and the
> interaction
> >>> energy (by g_energy tool) in my case?
> >> Interaction energy is a pairwise decomposition of short-range nonbonded
> >> interaction energy in the system. This energy is usually not physically
> >> meaningful, but if the force field has been parametrized in such a way
> >> that it is, the interaction energy is a contribution to the enthalpy of
> >> the system.
> >>
> > What forcefields embedded in GROMACS do, yes?
>
> AFAIK only CHARMM.
>
> > If coulomb energy is also existed between pairs, so the interaction
> energy
> > will be LJ+Coulomb yes?
>
> Pairs are 1-4 (intramolecular) interactions, so if you define
> interaction energy between two nonbonded species, you'll get zeroes for
> all the pair energies, by definition.
>
> > So what about PMF. It seems like an interaction energy too, but more
> > accurate one???
>
> That's not what a PMF is. A PMF is the change in free energy of a system
> as a function of progress along a reaction coordinate.
>
If interaction energy between protein1 and special ligand is more than
between protein2 and that ligand, it is tru its free energy would also be
more than it?

>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Gmx distance

[rose rahmani]

Hi,

I use gmx distance -dist 1.5 -f -s -n -o dist.xvg and select ZnS and
Protein-H groups.
Why i couldn't get any output file? Ot is processing during analuzing but
it doesn't have any dist.xvg and output file. When i use option -lt the
lifetime.xvg is empty. But i know there are distances closer than 1.5 nm
between ZnS and all non-hydrogwm atoms. How could it be possible?
I will be appreciatex if you help me.
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[gmx-users] Distance calculation

[rose rahmani]

Hi,

My system contains 20 amino acids around nanotube. I want to know the
adsorption amount of AA during simulation time; the adsorption occurs when
the distance between one of non-hydrogen atoms of AA and the tube surface
was less than 0.5 nm. So how can i calculate this property?

Would you please help me?
Best
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Re: [gmx-users] Gmx distance

[rose rahmani]

To be clear, i put 30 similar AA around NT i want to know how the average
distance of group PROTEIN( consist of 30 AA ) varies during 100nS
simulation. As i see in .gro file this distance decreased. I mean at the
first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE
MINIMUM LENGTH OF A LINE BETWEEN AA COM POINT AND Z AXIS OF NT, AS YOU CAN
IMAGINE THIS LINE IS PERPENDICULAR TO Z AXIS OF NT. this length is decrease
after 100nS. But what i can't understand is that when i analyze it by
g_dist( i select ZnS(NT) and Group Potein(=30 AA) in g_dist).. this is the
result!

Group 0 ( System) has 27831 elements
Group 1 (  Other) has   408 elements
Group 2 (ZnS) has   408 elements
Group 3 (Protein) has   720 elements
Group 4 (  Protein-H) has   390 elements
Group 5 (C-alpha) has30 elements
Group 6 (   Backbone) has90 elements
Group 7 (  MainChain) has90 elements
Group 8 (   MainChain+Cb) has   120 elements
Group 9 (MainChain+H) has   180 elements
Group10 (  SideChain) has   540 elements
Group11 (SideChain-H) has   300 elements
Group12 (Prot-Masses) has   720 elements
Group13 (non-Protein) has 27111 elements
Group14 (  Water) has 26703 elements
Group15 (SOL) has 26703 elements
Group16 (  non-Water) has  1128 elements

Select a group: 2
Selected 2: 'ZnS'
Select a group: 3
Selected 3: 'Protein'

   0.0000.2176011   -0.0120678   -0.04654980.2122209
   1.0000.2124534   -0.0301750   -0.04638700.2051198
   2.0000.1923753   -0.0158403   -0.05101350.1848106
   3.0000.1885315   -0.0107298   -0.04881600.1817856
   4.0000.2044982   -0.0052650   -0.04903290.1984630
   5.0000.2033602   -0.0002742   -0.04295370.1987720
   6.0000.20504870.0013833   -0.04446580.2001646
   7.0000.20024750.0041072   -0.04150030.1958568
   8.0000.20064730.0033450   -0.05118890.1939790
   9.0000.2032918   -0.119   -0.03300520.2005947
  10.0000.22556590.0003929   -0.04158570.2216990
  11.0000.22438110.0118313   -0.03447510.2214010
.
.
.
0.0000.6195676   -0.1357532   -0.00296350.6045051
1.0000.5355353   -0.37166000.01250200.3853707
2.0000.5243484   -0.36980010.01804520.3712997
3.0000.4459361   -0.1407223   -0.20213220.3717511
4.0000.5592619   -0.3545561   -0.21628430.3745463
5.0000.5707593   -0.3472078   -0.23097590.3896961
6.0000.5238984   -0.3467841   -0.01034190.3925600
7.0000.5122938   -0.33790520.00978730.3849275
8.0000.5608831   -0.3396225   -0.20521710.3963993
9.0000.5230988   -0.34793640.01726030.3902240
10.0000.5158455   -0.32838650.00471190.3977897

If the nanotube is along Z axis, so how g_dist calculate the COM of nano
tube? Is it each point along Z axis which pass center of nano tube or COM
in this case is just one point in the nanotube. If it is the second one, so
g_dist doesn't calculate perpendicular distance from AA to Z axis... so it
is completely different from what i want.

How can i get what i want?
this is exactly what want it is not an article it is just the figure 2
https://www.sciencedirect.com/science/article/pii/S0008622314006691#f0010


i'm completely confused!
Please help me

Best
Rose




On Wed, 7 Nov 2018, 18:32 Justin Lemkul 
>
> On 11/3/18 2:15 PM, rose rahmani wrote:
> > On Sat, 3 Nov 2018, 19:56 Justin Lemkul  >
> >>
> >> On 11/2/18 11:36 AM, rose rahmani wrote:
> >>> but this is output of -oall. its not a single value?!
> >> You are asking in your command for all interatomic distances between the
> >> groups (presumably, because you haven't shown your selection). This
> >> command won't yield what you're hoping to see and my advice does not
> >> apply for this type of situation (which doesn't seem to even match your
> >> original statement of your problem).
> >>
> >>> gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
> >>> # gmx distance is part of G R O M A C S:
> >>> #
> >>> #
> >>>
> >>
> ¸<8d><9a><9a><91>í<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><<
> >>> #
> >>> @title "Distance"
> >>> @xaxis  label "Time (ps)"
> >>> @yaxis  label "Distance (nm)"
>

[gmx-users] Mpirun continuing mdrun

[rose rahmani]

Hi,

I did 2ns simulation as an equilibration step by mdrun,

Mdrun -v -deffnm md1

and now i want to do product run for 100ns by mpirun,

Grompp -p -f -c md1.gro -t md1.cpt -o md2.tpr -maxwarn 1

Mpirun -np 8 mdrun -v -deffnm md2

but it will crush after few minutes at intialization...
Is that because i use mpirun?

Best
Rose
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Re: [gmx-users] Gmx distance

[rose rahmani]

On Sat, 3 Nov 2018, 19:56 Justin Lemkul 
>
> On 11/2/18 11:36 AM, rose rahmani wrote:
> > but this is output of -oall. its not a single value?!
>
> You are asking in your command for all interatomic distances between the
> groups (presumably, because you haven't shown your selection). This
> command won't yield what you're hoping to see and my advice does not
> apply for this type of situation (which doesn't seem to even match your
> original statement of your problem).
>
> >gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
> > # gmx distance is part of G R O M A C S:
> > #
> > #
> >
> ¸<8d><9a><9a><91>í<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><<
> > #
> > @title "Distance"
> > @xaxis  label "Time (ps)"
> > @yaxis  label "Distance (nm)"
> > @TYPE xy
> >
> >  1.0000.2290.2290.4460.5820.4460.2290.446
> > 0.5830.4470.2290.4470.2270.2280.2290.446
> > 0.5820.4460.2280.4460.5830.4470.2280.447
> > 0.2270.2270.2280.4460.5820.4460.2270.446
> > 0.5830.4470.2270.4470.2270.2280.2290.446
> > 0.5820.4460.2280.4460.5830.4470.2280.447
> > 0.2270.2280.2290.4460.5820.4460.2280.446
> > 0.5830.4470.2280.4470.2270.2290.2290.446
> > 0.5820.4460.2290.4460.5830.4470.2290.447
> > 0.2270.2290.2290.4460.5820.4460.2290.446
> > 0.5830.4470.2290.4470.2270.2280.2290.446
> > 0.5820.4460.2280.4460.5830.4470.2280.447
> > 0.2270.2280.2290.4460.5820.4460.2280.446
> > 0.5830.4470.2280.4470.2270.2270.2280.446
> > 0.5820.4460.2270.4460.5830.4470.2270.447
> > 0.2270.2280.2290.4460.5820.4460.2280.446
> > 0.5830.4470.2280.4
> > .
> > .
> > .
> >
> > and this is -o of g_dist;
> >   g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
> > #
> > # g_dist is part of G R O M A C S:
> > #
> > # GRowing Old MAkes el Chrono Sweat
> > #
> > @title "Distance"
> > @xaxis  label "Time (ps)"
> > @yaxis  label "Distance (nm)"
> > @TYPE xy
> > @ view 0.15, 0.15, 0.75, 0.85
> > @ legend on
> > @ legend box on
> > @ legend loctype view
> > @ legend 0.78, 0.8
> > @ legend length 2
> > @ s0 legend "|d|"
> > @ s1 legend "d\sx\N"
> > @ s2 legend "d\sy\N"
> > @ s3 legend "d\sz\N"
> > 0.0000.2176011   -0.0120678   -0.04654980.2122209
> > 1.0000.2124534   -0.0301750   -0.04638700.2051198
> > 2.0000.1923753   -0.0158403   -0.05101350.1848106
> > 3.0000.1885315   -0.0107298   -0.04881600.1817856
> > 4.0000.2044982   -0.0052650   -0.04903290.1984630
> > 5.0000.2033602   -0.0002742   -0.04295370.1987720
> > 6.0000.20504870.0013833   -0.04446580.2001646
> > 7.0000.20024750.0041072   -0.04150030.1958568
> > 8.0000.20064730.0033450   -0.05118890.1939790
> > 9.0000.2032918   -0.119   -0.03300520.2005947
> >10.0000.22556590.0003929   -0.04158570.2216990
> >11.0000.22438110.0118313   -0.03447510.2214010
> >12.0000.23478550.0078275   -0.03835320.2314994
> >13.0000.23715410.0081918   -0.03882670.2338107
>
> Here, you have what you want (I assume), and the first column after the
> time is all you need. It's the distance, which also can't be negative
> because it is the magnitude of the vector length and is unsigned.
>
How S0 is calculated? Does it resulted from distance between COM of amino
acid and COM of tube? Although, it is the magnitude of ... but it's
calculated from x,y,z which may be negative and were not abaolute?! In
addition, i put AAs (more than) 1.5 nm far from tube as an initial
configuration, but any 1.5 nm distance..???



> -Justin
>
> > .
> > .
> > .
> >
> >
> > On Thu, Nov 1, 2018 at 11:39 PM Justin 

Re: [gmx-users] Gmx distance

[rose rahmani]

but this is output of -oall. its not a single value?!

  gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
# gmx distance is part of G R O M A C S:
#
#
¸<8d><9a><9a><91>í<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><<
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy

1.0000.2290.2290.4460.5820.4460.2290.446
0.5830.4470.2290.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2270.2280.4460.5820.4460.2270.446
0.5830.4470.2270.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4470.2270.2290.2290.446
0.5820.4460.2290.4460.5830.4470.2290.447
0.2270.2290.2290.4460.5820.4460.2290.446
0.5830.4470.2290.4470.2270.2280.2290.446
0.5820.4460.2280.4460.5830.4470.2280.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4470.2270.2270.2280.446
0.5820.4460.2270.4460.5830.4470.2270.447
0.2270.2280.2290.4460.5820.4460.2280.446
0.5830.4470.2280.4
.
.
.

and this is -o of g_dist;
 g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
#
# g_dist is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@title "Distance"
@xaxis  label "Time (ps)"
@yaxis  label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
   0.0000.2176011   -0.0120678   -0.04654980.2122209
   1.0000.2124534   -0.0301750   -0.04638700.2051198
   2.0000.1923753   -0.0158403   -0.05101350.1848106
   3.0000.1885315   -0.0107298   -0.04881600.1817856
   4.0000.2044982   -0.0052650   -0.04903290.1984630
   5.0000.2033602   -0.0002742   -0.04295370.1987720
   6.0000.20504870.0013833   -0.04446580.2001646
   7.0000.20024750.0041072   -0.04150030.1958568
   8.0000.20064730.0033450   -0.05118890.1939790
   9.0000.2032918   -0.119   -0.03300520.2005947
  10.0000.22556590.0003929   -0.04158570.2216990
  11.0000.22438110.0118313   -0.03447510.2214010
  12.0000.23478550.0078275   -0.03835320.2314994
  13.0000.23715410.0081918   -0.03882670.2338107
.
.
.


On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul  wrote:

>
>
> On 11/1/18 2:25 PM, rose rahmani wrote:
> > I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
> > multiplied by (-), but how should i modify second column,i don't know how
> > s0 is calculated by g_distance to modify it??
>
> The output of -oall is a single value, the actual distance, which I
> assume is what you are talking about in your previous message. You can
> parse that column in any scripting language you like and
>
> [ pseudocode, not functional ]
> if (value < 0)
> {
>  value *= -1
> }
>
> -Justin
> > On Wed, 31 Oct 2018, 19:38 Justin Lemkul,  wrote:
> >
> >>
> >> On 10/31/18 12:06 PM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to calculate distances between fixed tube in the middle of the
> box
> >>> and amino acids(all are same type)around it. But gmx distance gives me
> >> the
> >>> relative distance i mean AA can be front or back( can be 0.5 or -0.5
> from
> >>> tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have the
> >>> absolute value of distances?
> >>> Would you please help me?
> >> Write a simple post-processing script that multiplies any negative value
> >> by -1.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
&g

Re: [gmx-users] Gmx distance

[rose rahmani]

I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
multiplied by (-), but how should i modify second column,i don't know how
s0 is calculated by g_distance to modify it??

On Wed, 31 Oct 2018, 19:38 Justin Lemkul,  wrote:

>
>
> On 10/31/18 12:06 PM, rose rahmani wrote:
> > Hi,
> >
> > I want to calculate distances between fixed tube in the middle of the box
> > and amino acids(all are same type)around it. But gmx distance gives me
> the
> > relative distance i mean AA can be front or back( can be 0.5 or -0.5 from
> > tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have the
> > absolute value of distances?
> > Would you please help me?
>
> Write a simple post-processing script that multiplies any negative value
> by -1.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.
>
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Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[rose rahmani]

Oh, yes. I've got t now!
Thank you so much Justin for your kind responses(as always;)).

On Thu, Nov 1, 2018 at 12:23 AM Justin Lemkul  wrote:

>
>
> On 10/31/18 4:23 PM, rose rahmani wrote:
> >   i've tried it.But the results are exactly the same as i didn't apply
> > patches. it doesn't make any difference. So what is the purpose of using
> > -ter (COO- & NH3) when results are same in my case?
>
> I don't follow. Topology generation requires the selection of terminal
> patching of some sort, either if pdb2gmx does it for you (choosing
> defaults) or if you do it.
>
> -Justin
>
> > On Wed, 31 Oct 2018, 22:49 Justin Lemkul,  wrote:
> >
> >>
> >> On 10/31/18 2:56 PM, rose rahmani wrote:
> >>> Thank you, but I couldn't understand you exactly. My structures already
> >>> have NH3+ and COO- . You mean everything is right? That's normal, yes?
> >> I was stating which terminal patches you should choose with pdb2gmx to
> >> transform the Phe .rtp topology into that of a zwitterion.
> >>
> >> -Justin
> >>
> >>> On Wed, 31 Oct 2018, 21:43 Justin Lemkul,  wrote:
> >>>
> >>>> On 10/31/18 2:01 PM, rose rahmani wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I want to use zwitterionic form of AAs in CHARMM ff. I gave structure
> >> in
> >>>>> Discovery studio and then use pdb2gmx to get its topology and ...
> >> files.
> >>>>> But the number of atoms in topol.top and also some atom's partial
> >> charges
> >>>>> are different from atoms and charges in aminoacids.rtp
> >>>>> For example, in the case of phenylalanine,
> >>>>> this is topology file after pdb2gmx:
> >>>>>
> >>>>> [ atoms ]
> >>>>> ;   nr   type  resnr residue  atom   cgnr charge   mass
> >>>> typeB
> >>>>>  chargeB  massB
> >>>>> ; residue   1 PHE rtp PHE  q  0.0
> >>>>> 1NH3  1PHE  N  1   -0.3
>  14.007
> >>   ;
> >>>>> qtot -0.3
> >>>>> 2 HC  1PHE H1  2   0.33
> 1.008
> >>   ;
> >>>>> qtot 0.03
> >>>>> 3 HC  1PHE H2  3   0.33
> 1.008
> >>   ;
> >>>>> qtot 0.36
> >>>>> 4 HC  1PHE H3  4   0.33
> 1.008
> >>   ;
> >>>>> qtot 0.69
> >>>>> 5CT1  1PHE CA  5   0.21
>  12.011
> >>   ;
> >>>>> qtot 0.9
> >>>>> 6 HB  1PHE HA  60.1
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>> 7CT2  1PHE CB  7  -0.18
>  12.011
> >>   ;
> >>>>> qtot 0.82
> >>>>> 8 HA  1PHEHB1  8   0.09
> 1.008
> >>   ;
> >>>>> qtot 0.91
> >>>>> 9 HA  1PHEHB2  9   0.09
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>>10 CA  1PHE CG 10  0
>  12.011
> >>   ;
> >>>>> qtot 1
> >>>>>11 CA  1PHECD1 11 -0.115
>  12.011
> >>   ;
> >>>>> qtot 0.885
> >>>>>12 HP  1PHEHD1 12  0.115
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>>13 CA  1PHECE1 13 -0.115
>  12.011
> >>   ;
> >>>>> qtot 0.885
> >>>>>14 HP  1PHEHE1 14  0.115
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>>15 CA  1PHE CZ 15 -0.115
>  12.011
> >>   ;
> >>>>> qtot 0.885
> >>>>>16 HP  1PHE HZ 16  0.115
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>>17 CA  1PHECD2 17 -0.115
>  12.011
> >>   ;
> >>>>> qtot 0.885
> >>>>>18 HP  1PHEHD2 18  0.115
> 1.008
> >>   ;
> >>>>> qtot 1
> >>>>>19 CA  

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[rose rahmani]

 i've tried it.But the results are exactly the same as i didn't apply
patches. it doesn't make any difference. So what is the purpose of using
-ter (COO- & NH3) when results are same in my case?

On Wed, 31 Oct 2018, 22:49 Justin Lemkul,  wrote:

>
>
> On 10/31/18 2:56 PM, rose rahmani wrote:
> > Thank you, but I couldn't understand you exactly. My structures already
> > have NH3+ and COO- . You mean everything is right? That's normal, yes?
>
> I was stating which terminal patches you should choose with pdb2gmx to
> transform the Phe .rtp topology into that of a zwitterion.
>
> -Justin
>
> >
> > On Wed, 31 Oct 2018, 21:43 Justin Lemkul,  wrote:
> >
> >>
> >> On 10/31/18 2:01 PM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to use zwitterionic form of AAs in CHARMM ff. I gave structure
> in
> >>> Discovery studio and then use pdb2gmx to get its topology and ...
> files.
> >>> But the number of atoms in topol.top and also some atom's partial
> charges
> >>> are different from atoms and charges in aminoacids.rtp
> >>> For example, in the case of phenylalanine,
> >>> this is topology file after pdb2gmx:
> >>>
> >>> [ atoms ]
> >>> ;   nr   type  resnr residue  atom   cgnr charge   mass
> >> typeB
> >>> chargeB  massB
> >>> ; residue   1 PHE rtp PHE  q  0.0
> >>>1NH3  1PHE  N  1   -0.3 14.007
>  ;
> >>> qtot -0.3
> >>>2 HC  1PHE H1  2   0.33  1.008
>  ;
> >>> qtot 0.03
> >>>3 HC  1PHE H2  3   0.33  1.008
>  ;
> >>> qtot 0.36
> >>>4 HC  1PHE H3  4   0.33  1.008
>  ;
> >>> qtot 0.69
> >>>5CT1  1PHE CA  5   0.21 12.011
>  ;
> >>> qtot 0.9
> >>>6 HB  1PHE HA  60.1  1.008
>  ;
> >>> qtot 1
> >>>7CT2  1PHE CB  7  -0.18 12.011
>  ;
> >>> qtot 0.82
> >>>8 HA  1PHEHB1  8   0.09  1.008
>  ;
> >>> qtot 0.91
> >>>9 HA  1PHEHB2  9   0.09  1.008
>  ;
> >>> qtot 1
> >>>   10 CA  1PHE CG 10  0 12.011
>  ;
> >>> qtot 1
> >>>   11 CA  1PHECD1 11 -0.115 12.011
>  ;
> >>> qtot 0.885
> >>>   12 HP  1PHEHD1 12  0.115  1.008
>  ;
> >>> qtot 1
> >>>   13 CA  1PHECE1 13 -0.115 12.011
>  ;
> >>> qtot 0.885
> >>>   14 HP  1PHEHE1 14  0.115  1.008
>  ;
> >>> qtot 1
> >>>   15 CA  1PHE CZ 15 -0.115 12.011
>  ;
> >>> qtot 0.885
> >>>   16 HP  1PHE HZ 16  0.115  1.008
>  ;
> >>> qtot 1
> >>>   17 CA  1PHECD2 17 -0.115 12.011
>  ;
> >>> qtot 0.885
> >>>   18 HP  1PHEHD2 18  0.115  1.008
>  ;
> >>> qtot 1
> >>>   19 CA  1PHECE2 19 -0.115 12.011
>  ;
> >>> qtot 0.885
> >>>   20 HP  1PHEHE2 20  0.115  1.008
>  ;
> >>> qtot 1
> >>>   21 CC  1PHE  C 21   0.34 12.011
>  ;
> >>> qtot 1.34
> >>>   22 OC  1PHEOT1 22  -0.67 15.999
>  ;
> >>> qtot 0.67
> >>>   23 OC  1PHEOT2 23  -0.67 15.999
>  ;
> >>> qtot 0
> >>>
> >>> and this is .rtp file for PHE:
> >>>
> >>> [ PHE ]
> >>>[ atoms ]
> >>>   N   NH1 -0.47   0
> >>>   HN  H   0.311
> >>>   CA  CT1 0.072
> >>>   HA  HB  0.093
> >>>   CB  CT2 -0.18   4
> >>>   HB1 HA  0.095
> >>>   HB2 HA  0.096
> >>>   CG  CA  0.00

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[rose rahmani]

Thank you, but I couldn't understand you exactly. My structures already
have NH3+ and COO- . You mean everything is right? That's normal, yes?


On Wed, 31 Oct 2018, 21:43 Justin Lemkul,  wrote:

>
>
> On 10/31/18 2:01 PM, rose rahmani wrote:
> > Hi,
> >
> > I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in
> > Discovery studio and then use pdb2gmx to get its topology and ... files.
> > But the number of atoms in topol.top and also some atom's partial charges
> > are different from atoms and charges in aminoacids.rtp
> > For example, in the case of phenylalanine,
> > this is topology file after pdb2gmx:
> >
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeB
> >chargeB  massB
> > ; residue   1 PHE rtp PHE  q  0.0
> >   1NH3  1PHE  N  1   -0.3 14.007   ;
> > qtot -0.3
> >   2 HC  1PHE H1  2   0.33  1.008   ;
> > qtot 0.03
> >   3 HC  1PHE H2  3   0.33  1.008   ;
> > qtot 0.36
> >   4 HC  1PHE H3  4   0.33  1.008   ;
> > qtot 0.69
> >   5CT1  1PHE CA  5   0.21 12.011   ;
> > qtot 0.9
> >   6 HB  1PHE HA  60.1  1.008   ;
> > qtot 1
> >   7CT2  1PHE CB  7  -0.18 12.011   ;
> > qtot 0.82
> >   8 HA  1PHEHB1  8   0.09  1.008   ;
> > qtot 0.91
> >   9 HA  1PHEHB2  9   0.09  1.008   ;
> > qtot 1
> >  10 CA  1PHE CG 10  0 12.011   ;
> > qtot 1
> >  11 CA  1PHECD1 11 -0.115 12.011   ;
> > qtot 0.885
> >  12 HP  1PHEHD1 12  0.115  1.008   ;
> > qtot 1
> >  13 CA  1PHECE1 13 -0.115 12.011   ;
> > qtot 0.885
> >  14 HP  1PHEHE1 14  0.115  1.008   ;
> > qtot 1
> >  15 CA  1PHE CZ 15 -0.115 12.011   ;
> > qtot 0.885
> >  16 HP  1PHE HZ 16  0.115  1.008   ;
> > qtot 1
> >  17 CA  1PHECD2 17 -0.115 12.011   ;
> > qtot 0.885
> >  18 HP  1PHEHD2 18  0.115  1.008   ;
> > qtot 1
> >  19 CA  1PHECE2 19 -0.115 12.011   ;
> > qtot 0.885
> >  20 HP  1PHEHE2 20  0.115  1.008   ;
> > qtot 1
> >  21 CC  1PHE  C 21   0.34 12.011   ;
> > qtot 1.34
> >  22 OC  1PHEOT1 22  -0.67 15.999   ;
> > qtot 0.67
> >  23 OC  1PHEOT2 23  -0.67 15.999   ;
> > qtot 0
> >
> > and this is .rtp file for PHE:
> >
> > [ PHE ]
> >   [ atoms ]
> >  N   NH1 -0.47   0
> >  HN  H   0.311
> >  CA  CT1 0.072
> >  HA  HB  0.093
> >  CB  CT2 -0.18   4
> >  HB1 HA  0.095
> >  HB2 HA  0.096
> >  CG  CA  0.007
> >  CD1 CA  -0.115  8
> >  HD1 HP  0.115   9
> >  CE1 CA  -0.115  10
> >  HE1 HP  0.115   11
> >  CZ  CA  -0.115  12
> >  HZ  HP  0.115   13
> >  CD2 CA  -0.115  14
> >  HD2 HP  0.115   15
> >  CE2 CA  -0.115  16
> >  HE2 HP  0.115   17
> >  C   C   0.5118
> >  O   O   -0.51   19
> > so as you see there O and 2 H more...  . I know that's because of COO
> group
> > and HH.. but which of them are the real structure of zwitterionic form of
> >   amino acid in force field? are both true? I would be appreciated if you
> > can help me.
>
> Just apply the normal NH3+ and COO- terminal patches. There are no
> special zwitterion patches like in some force fields (OPLS, etc.)
> Naturally, the .rtp will change - that is the function of the .tdb entries.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
&g

[gmx-users] Zwitterionic amino acid topology parameters in CHARMM

[rose rahmani]

Hi,

I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in
Discovery studio and then use pdb2gmx to get its topology and ... files.
But the number of atoms in topol.top and also some atom's partial charges
are different from atoms and charges in aminoacids.rtp
For example, in the case of phenylalanine,
this is topology file after pdb2gmx:

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB
; residue   1 PHE rtp PHE  q  0.0
 1NH3  1PHE  N  1   -0.3 14.007   ;
qtot -0.3
 2 HC  1PHE H1  2   0.33  1.008   ;
qtot 0.03
 3 HC  1PHE H2  3   0.33  1.008   ;
qtot 0.36
 4 HC  1PHE H3  4   0.33  1.008   ;
qtot 0.69
 5CT1  1PHE CA  5   0.21 12.011   ;
qtot 0.9
 6 HB  1PHE HA  60.1  1.008   ;
qtot 1
 7CT2  1PHE CB  7  -0.18 12.011   ;
qtot 0.82
 8 HA  1PHEHB1  8   0.09  1.008   ;
qtot 0.91
 9 HA  1PHEHB2  9   0.09  1.008   ;
qtot 1
10 CA  1PHE CG 10  0 12.011   ;
qtot 1
11 CA  1PHECD1 11 -0.115 12.011   ;
qtot 0.885
12 HP  1PHEHD1 12  0.115  1.008   ;
qtot 1
13 CA  1PHECE1 13 -0.115 12.011   ;
qtot 0.885
14 HP  1PHEHE1 14  0.115  1.008   ;
qtot 1
15 CA  1PHE CZ 15 -0.115 12.011   ;
qtot 0.885
16 HP  1PHE HZ 16  0.115  1.008   ;
qtot 1
17 CA  1PHECD2 17 -0.115 12.011   ;
qtot 0.885
18 HP  1PHEHD2 18  0.115  1.008   ;
qtot 1
19 CA  1PHECE2 19 -0.115 12.011   ;
qtot 0.885
20 HP  1PHEHE2 20  0.115  1.008   ;
qtot 1
21 CC  1PHE  C 21   0.34 12.011   ;
qtot 1.34
22 OC  1PHEOT1 22  -0.67 15.999   ;
qtot 0.67
23 OC  1PHEOT2 23  -0.67 15.999   ;
qtot 0

and this is .rtp file for PHE:

[ PHE ]
 [ atoms ]
N   NH1 -0.47   0
HN  H   0.311
CA  CT1 0.072
HA  HB  0.093
CB  CT2 -0.18   4
HB1 HA  0.095
HB2 HA  0.096
CG  CA  0.007
CD1 CA  -0.115  8
HD1 HP  0.115   9
CE1 CA  -0.115  10
HE1 HP  0.115   11
CZ  CA  -0.115  12
HZ  HP  0.115   13
CD2 CA  -0.115  14
HD2 HP  0.115   15
CE2 CA  -0.115  16
HE2 HP  0.115   17
C   C   0.5118
O   O   -0.51   19
so as you see there O and 2 H more...  . I know that's because of COO group
and HH.. but which of them are the real structure of zwitterionic form of
 amino acid in force field? are both true? I would be appreciated if you
can help me.

Best
-- 
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[gmx-users] Gmx distance

[rose rahmani]

Hi,

I want to calculate distances between fixed tube in the middle of the box
and amino acids(all are same type)around it. But gmx distance gives me the
relative distance i mean AA can be front or back( can be 0.5 or -0.5 from
tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have the
absolute value of distances?
Would you please help me?

Best
-- 
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[gmx-users] Gmx distance

[rose rahmani]

Hi,

I want to calculate distances between fixed tube in the middle of the box
and amino acids(all are same type)around it. But gmx distance gives me the
relative distance i mean AA can be front or back( can be 0.5 or -0.5 from
tube) of  tube but still |-0.5|=0.5 nm far from it. How can i have the
absolute value of distances?
Would you please help me?

Best
Rose
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Re: [gmx-users] Topology file

[rose rahmani]

First, i think it's better to ask WHY
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
That's why people use position restraints.

About WHEN,  sometimes your molecule behavior is different in
box. For instance you study the interaction of your molecule with surface.
So the molecule need to be free and move in a box to find its best
configuration toward surface. Because its properties may differ in
different part of box. You can't put a restriction on it, because it's
distance and configuration, is crucial in interacting with surface...
Maybe it's not a scientific explanation of an issue( as justin masterly do)
but i just tried to share my experience. Hope it helps!

Best

Rose



On Wed, 10 Oct 2018, 16:21 Mahdi Sobati Nezhad, 
wrote:

> Thanks rose. Can you tell me more about which cases I should use position
> restrictions?!
> Thanks
>
> On Fri, 5 Oct 2018 10:33 rose rahmani,  wrote:
>
> > Hi,
> >
> > It depends on you, wheter you want to put position restriction on your
> > molecule you should add posre.itp to topol.top or not.
> > But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read
> > posre.itp files in topol.top an apply position restriction to molecule.
> >
> > Rose
> >
> > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, <
> > mahdisobatinez...@gmail.com>
> > wrote:
> >
> > > Hello Gromacs users.
> > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there
> > is
> > > no any porse.itp
> > > What can I do?!
> > > Do it's important that porse.itp should be in topol.top or its enough
> > that
> > > pdb2gmx make porse.itp?!
> > >
> > > Thanks
> > > --
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[gmx-users] gmx distance

[rose rahmani]

Hi

I have 30 similar amino acid around nanotune and i want to calculate the
average distance of all of them(i put all of AA in group of Protein in
index file and define them as 30 chain of protein means i have defined them
as Protein, Protein2, Protein3,...Protein30 in topol.top ) from
(infinite)NT during simulation. i used g_dist but as you now it calculates
COM distance of Protein and NT. but the COM of NT is just one point in the
NT so g_dist calculate the distance between COM of Protein and NT.(if
protein was closer to beginning of NT the distance(that g_dist show) will
be much different from when it's in middle part of NT( because at this time
Protein is maybe at the top of COM of NT,... )). but i want the distance
between Zaxis of NT to average distance of Protein(which is coleceted of 30
similar amino acids). So what should i do? i refer you to this picture(top).
https://ars.els-cdn.com/content/image/1-s2.0-S0008622314006691-gr2.sml

Would you please help me?

Best
Rose
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Re: [gmx-users] Topology file

[rose rahmani]

Hi,

It depends on you, wheter you want to put position restriction on your
molecule you should add posre.itp to topol.top or not.
But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read
posre.itp files in topol.top an apply position restriction to molecule.

Rose

On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, 
wrote:

> Hello Gromacs users.
> When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there is
> no any porse.itp
> What can I do?!
> Do it's important that porse.itp should be in topol.top or its enough that
> pdb2gmx make porse.itp?!
>
> Thanks
> --
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Re: [gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

[rose rahmani]

As far as i know NO.
You want the adsorption energy which needs an accurate sampling of protein
in different distances and calculating energy for each sample and then 
BTW, i think calculating this quantity for a big molecule like protein is
not a great idea. I think you need to do long time simulation and then find
out which residue/s are closer to nanotube most of the time and calculate
interaction energy or for more real adsorption energy cut that residue/s
and use umbrella sampling...

Rose



On Sat, 29 Sep 2018, 10:27 Sundari,  wrote:

> Hi,
> Is there any  other way for example calculation of binding energy by my
> existed files (normal MD .trr and .edr files) generated by gromacs  instead
> of restart a simulation. Because currently  I am not familiar with the
>  umbrella sampling and have urgent need of energies.
> Please suggest any idea.
>
> sundari
>
>
>
>
> On Fri, Sep 28, 2018 at 8:47 PM rose rahmani 
> wrote:
>
> > Hi,
> >
> > You can calculate adsorption energy by umbrella sampling.
> > http://www.mdtutorials.com/gmx/umbrella/index.html
> > .edr just gives you the interaction energy not adsorption energy and
> > distance.
> >
> > Rose
> >
> > On Fri, Sep 28, 2018 at 6:37 PM Sundari  wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I want to calculate Binding energy between the protein and the carbon
> > nano
> > > tube. Is there any way  to do that by gromacs commands.
> > >  As I only have .xtc and .tpr files from gromacs.
> > >
> > > Please suggest me any idea or any article so that based on trajectories
> > > (xtc or trr) how one can get these binding energies.
> > >
> > > Regards,
> > > Sundar
> > > --
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Re: [gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

[rose rahmani]

Hi,

You can calculate adsorption energy by umbrella sampling.
http://www.mdtutorials.com/gmx/umbrella/index.html
.edr just gives you the interaction energy not adsorption energy and
distance.

Rose

On Fri, Sep 28, 2018 at 6:37 PM Sundari  wrote:

> Dear Gromacs users,
>
> I want to calculate Binding energy between the protein and the carbon nano
> tube. Is there any way  to do that by gromacs commands.
>  As I only have .xtc and .tpr files from gromacs.
>
> Please suggest me any idea or any article so that based on trajectories
> (xtc or trr) how one can get these binding energies.
>
> Regards,
> Sundar
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[gmx-users] Constraint bonds

[rose rahmani]

Hi,

I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond,
Mn-O bond,... formed. Now i want to do MD simulation for this
functionalized nanotube. (I use AMBER99SB ff)

How should i define ffbonded.itp?I have bond length and angles but i don't
know kb. If for example kb of Mn-O for another similar structures exists in
literatures can i use them?
If kb doesn't exist, can i freeze this BOND(not the whole AA) on known bond
length, ANGLE on known dihedral angle and known partial charges charges(all
achieved after functionalization of NT with AA by DFT) or maybe constraint
it?
Is it possible to freeze bond at all?! Is there any better choice?


Would you please help and correct me?

Best regards
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[gmx-users] Freeze and constraint bond

[rose rahmani]

Hi,

I have functionalized Mn-cdS nanotube by amino acid,... . New O-S bond,
Mn-O bond,... formed. Now i want to do MD simulation for this
functionalized nanotube. (I use AMBER99SB ff)

How should i define ffbonded.itp?I have bond length and angles but i don't
know kb. If for example kb of Mn-O for another similar structures exists in
literatures can i use them?
If kb doesn't exist, can i freeze this BOND(not the whole AA) on known bond
length, ANGLE on known dihedral angle and known partial charges charges(all
achieved after functionalization of NT with AA by DFT) or maybe constraint
it?
Is it possible to freeze bond at all?! Is there any better choice?


Would you please help and correct me?

Best regards
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[gmx-users] Your message to gromacs.org_gmx-users awaits moderator approval

[rose rahmani]

Hi,

I recieved an email from GROMACS, says the message is too big(because of
many replies). So what should i do to continue my discussion?

Best
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Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

hat the reference is a surface gmx gangle might work.
> Notice
> > >> that I wrote might, because I believe it will still be cumbersome for
> > the
> > >> many water molecules in the box. For the example of the two planes,
> you
> > >> just basically need to set "-g1 plane", "-g2 plane" and pass the
> > >> selections
> > >> of the surface and water molecule H-O-H plane to "-group1" and
> > "-group2",
> > >> respectively. For the example of the surface and the H-O vector, you
> > adapt
> > >> it accordingly ("-g1 plane", "-g2 vector" and the corresponding
> > >> selections). I easily can see this working for a single water
> molecule,
> > >> but
> > >> for all the water molecules in the box this might get tricky.
> Specially
> > if
> > >> you're gonna try to tackle them all under a single selection. You
> could
> > >> aways run the command in a loop for each water molecule in the box,
> but
> > >> that doesn't look very "smart" and/or fast.
> > >>
> > >> I'd still probably look into doing my own code using some third party
> > >> module/package to parse and analyze trajectories.
> > >>
> > >> J
> > >>
> > >> On Wed, Sep 12, 2018 at 5:01 PM rose rahmani 
> > >> wrote:
> > >>
> > >> > On Wed, 12 Sep 2018, 19:13 João Henriques, <
> > >> joao.m.a.henriq...@gmail.com>
> > >> > wrote:
> > >> >
> > >> > > "It gives me the histogram of angles" ---> what is "it" in this
> > >> sentence?
> > >> > >
> > >> > It= -oh output of gmx gangle which writes the histogram of 'angleS'
> > not
> > >> the
> > >> > angle that i have already defined.( THE beta angle= angle between
> HOH
> > >> plane
> > >> > of water molecules and surface plane , THE alpha angke= angle
> between
> > >> OH of
> > >> > water molecules and surface plane. The surface is ZnS surface(i have
> > an
> > >> > slab of ZnS) not protein.
> > >> >
> > >> > > There are 26 emails on the link I shared. What did you actually
> > try? I
> > >> > > mean, an histogram and a distribution function aren't that far
> > >> apart...
> > >> > > Also, I believe understand what you want to do, you want to
> > calculate
> > >> the
> > >> > > ADF of the water molecules with the protein surface as the
> > reference.
> > >> > > Something
> > >> > > like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see
> > >> Figures
> > >> > 3
> > >> > > and 5). Well, I've played around with a similar problem and
> there's
> > no
> > >> > > simple answer. I ended up using MDAnalysis
> > >> > > <
> > >> > >
> > >> >
> > >>
> >
> https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html
> > >> > > >
> > >> > > (click on the link, see 4.8.3.1.3. AngularDistribution).
> > >> >
> > >>
> > > How can i use it in gromacs?
> > >
> > >> > Thank you.
> > >> >
> > >> > > I tried doing the
> > >> > > same with the native Gromacs tools but found it too be too much
> of a
> > >> pain
> > >> > > in the a**.
> > >> > >
> > >> > I think gromacs can do it. But first i should define all O-H and in
> > box
> > >> > then calculate the angle between  for ALPHA
> > >> > Maybe should define H-O-H plane then for BETA).
> > >> >
> > >> > I found the documentation of gmx gangle gmx angle so complicated and
> > >> > confusing. I don't know how can i hsethem priperly...
> > >> >
> > >> > Best
> > >> >
> > >> > >
> > >> > > I hope this is at least somewhat useful.
> > >> > >
> > >> > > Cheers,
> > >> > > João
> > >> > >
> > >> > >
> > >> > >
> > >> > > On Wed, Sep 12, 2018 at 3:41 PM rose rahmani <
> rose.rhm...@gmail.com
> > >
> > >&g

[gmx-users] Umbrella sampling histograms.

[rose rahmani]

Hi,

I did umbrella sampling for different distances of amino acid  above
surface.
I found i special distance (1-1.2 nm above surface)histograms  does not
overlap. I did the sampling several times even for each 0.001 nm( of the
distane between 1-1.2 nm) but the histo.xvg file didn't show ANY changes in
that distance.
When you see in histo.xvg file that there isn't any data in 1nm, is that
really 1nm??? Because the histo file begins and ends  from 0.8 difference
in comparision to real distances. I MEAN, i choosed distances between 1nm
and 1.7 nm to sample. But histogram shows the windows from 0.2 nm to 1.78
nm. I think it's normal because each curve have width so when i choose 1nm
infact gives histo between 0.6 to 1.4 which depends to force constant.is it
true?


 My question is that:
1- in my case i don't have any curve in 1-1.2 nm. Should i choose really
distances 1 to 1.2 nm from summarydistances file?

2- as i told before, i sample different distances between 1-1.2, but i
couldn't find any change in histo.xvg file and for profile.xvg file at 1.1
nm there is an odd number for energy(too high)  which shows the discrepency
and discontinuity in sampling.

3-does it mean the amino acid doesn't stay in 1-1.2 nm? If yes, so why i
see this distance in summarydistances.dat file?

Maybe my explanation is  a little bit confusing;) but hope to be clear...


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Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

On Wed, 12 Sep 2018, 19:13 João Henriques, 
wrote:

> "It gives me the histogram of angles" ---> what is "it" in this sentence?
>
It= -oh output of gmx gangle which writes the histogram of 'angleS' not the
angle that i have already defined.( THE beta angle= angle between HOH plane
of water molecules and surface plane , THE alpha angke= angle between OH of
water molecules and surface plane. The surface is ZnS surface(i have an
slab of ZnS) not protein.

> There are 26 emails on the link I shared. What did you actually try? I
> mean, an histogram and a distribution function aren't that far apart...
> Also, I believe understand what you want to do, you want to calculate the
> ADF of the water molecules with the protein surface as the reference.
> Something
> like this <https://pubs.acs.org/doi/abs/10.1021/jp0604241> (see Figures 3
> and 5). Well, I've played around with a similar problem and there's no
> simple answer. I ended up using MDAnalysis
> <
> https://www.mdanalysis.org/docs/documentation_pages/analysis/waterdynamics.html
> >
> (click on the link, see 4.8.3.1.3. AngularDistribution).

Thank you.

> I tried doing the
> same with the native Gromacs tools but found it too be too much of a pain
> in the a**.
>
I think gromacs can do it. But first i should define all O-H and in box
then calculate the angle between  for ALPHA
Maybe should define H-O-H plane then for BETA).

I found the documentation of gmx gangle gmx angle so complicated and
confusing. I don't know how can i hsethem priperly...

Best

>
> I hope this is at least somewhat useful.
>
> Cheers,
> João
>
>
>
> On Wed, Sep 12, 2018 at 3:41 PM rose rahmani 
> wrote:
>
> > Thank you Joao,
> >
> > On Wed, 12 Sep 2018, 14:04 João Henriques,  >
> > wrote:
> >
> > > Dear Rose,
> > >
> > > Spamming is not the answer. There have been quite a few threads about
> > this
> > > subject in the recent past. Searching the mailing list before posting
> is
> > > usually good practice. If then something remains unclear, please feel
> > free
> > > to ask. I remember having quite long discussions with a Dilip H. N.
> about
> > > this subject (on and off the mailing list).
> > >
> > > A simple query fetched 26 results:
> > >
> > >
> >
> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0
> >
> > I search and read about but it didn't help me. It gives me the histogram
> of
> > angles but what i really want is the distribituion of special defined
> > angle(between two plane) during simulation. I refer you ahain to
> >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface?_ec=topicPostOverviewAuthoredQuestions&_sg=hV7QNgmmW-MkZF5OKfgZlaI5O0G5HeVQGSGoneQ1gDaXV_96qBhs2Re6IrsBNcXYMTf0FzIqXPyDrI9r.8ylTJZVEy00BT4mPuq0m2nGK5dREPBjukd2plNMaXf5ocFCOJCRriPhzJum_Vt2KLoZVmTZVBDoQZQOcBKAP8EU
> >
> >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
> >
> >  I asked different questions several times last 2 days and i thought my
> > email doesn't recieve and share in mailing-list.
> >
> > I'm really confused about what people suggest. I'm a student and i
> think, i
> > clearly explained what i want after huge searches, it's not because of
> > indolence and i would be appreciated if any one could answer me.
> >
> > Regards
> >
> >
> >
> > > Play with the query a bit and it should get you a lot of info on your
> > > problem.
> > >
> > > Best regards,
> > > João
> > >
> > >
> > >
> > >
> > >
> > > On Mon, Sep 10, 2018 at 10:29 AM rose rahmani 
> > > wrote:
> > >
> > > > Hi,
> > > > How can i calculate the angular distribution of the angles between
> > water
> > > > molecule water and surface? surface during molecular dynamics
> > simulation?
> > > >  is it possible by GROMACS? gmx gangle?
> > > >
> > > > would you please help me?
> > > >
> > > > To be clear; i refer you to these plots
> > > >
> > > >
> > >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
> > > >
> > > >
> > > > Best regards
> > > >
> > > > Rose
> > > > --
> > >

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

Thank you Joao,

On Wed, 12 Sep 2018, 14:04 João Henriques, 
wrote:

> Dear Rose,
>
> Spamming is not the answer. There have been quite a few threads about this
> subject in the recent past. Searching the mailing list before posting is
> usually good practice. If then something remains unclear, please feel free
> to ask. I remember having quite long discussions with a Dilip H. N. about
> this subject (on and off the mailing list).
>
> A simple query fetched 26 results:
>
> https://www.mail-archive.com/search?l=gromacs.org_gmx-users%40maillist.sys.kth.se=dilip+h+n+angle=0=0

I search and read about but it didn't help me. It gives me the histogram of
angles but what i really want is the distribituion of special defined
angle(between two plane) during simulation. I refer you ahain to
https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface?_ec=topicPostOverviewAuthoredQuestions&_sg=hV7QNgmmW-MkZF5OKfgZlaI5O0G5HeVQGSGoneQ1gDaXV_96qBhs2Re6IrsBNcXYMTf0FzIqXPyDrI9r.8ylTJZVEy00BT4mPuq0m2nGK5dREPBjukd2plNMaXf5ocFCOJCRriPhzJum_Vt2KLoZVmTZVBDoQZQOcBKAP8EU

https://www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface

 I asked different questions several times last 2 days and i thought my
email doesn't recieve and share in mailing-list.

I'm really confused about what people suggest. I'm a student and i think, i
clearly explained what i want after huge searches, it's not because of
indolence and i would be appreciated if any one could answer me.

Regards



> Play with the query a bit and it should get you a lot of info on your
> problem.
>
> Best regards,
> João
>
>
>
>
>
> On Mon, Sep 10, 2018 at 10:29 AM rose rahmani 
> wrote:
>
> > Hi,
> > How can i calculate the angular distribution of the angles between water
> > molecule water and surface? surface during molecular dynamics simulation?
> >  is it possible by GROMACS? gmx gangle?
> >
> > would you please help me?
> >
> > To be clear; i refer you to these plots
> >
> >
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
> >
> >
> > Best regards
> >
> > Rose
> > --
> > 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.
> >
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[gmx-users] Angle between two plane

[rose rahmani]

Hi,

Hiw can i calculate angle between two plane?(HOH plane of water and surface
plane or perpendicular axis to it? How should i make an index for defining
HOH plane?

Best
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Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

On Mon, 10 Sep 2018, 12:58 rose rahmani,  wrote:

> Hi,
> How can i calculate the angular distribution of the angles between water
> molecule water and surface? surface during molecular dynamics simulation?
>  is it possible by GROMACS? gmx gangle?
>
> would you please help me?
>
> To be clear; i refer you to these plots
>
> https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface
>
>
> Best regards
>
> Rose
>
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[gmx-users] Fwd: Gmx gangle

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Sun, 9 Sep 2018, 14:45
Subject: Gmx gangle
To: 


Hi,

I want to calculate angle between water molecules and ZnS surface(slab). I
mean the angular distribution function(ADF) of ALPHA and BETA. I define to
angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
angle between HOH plane and surface(plane).

I used gmax gangle for Alpha:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
Then i selected water(SOL) group

For Beta:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
And again i selected water group.

But results are little odd and histograms are two plot which are symmetric
plots.

I think sth is wrong. Should i make an index file for OH bond in the case
of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
calculated the angle between COM of water vector and surface not the OH
bond of water. As you know water has 2 OH bond. So... what should i do?

How about BETA? does it really calculate what i want?

Should i make an special index file?

If i want to calculate this property (ADF) in for example 1 nm from
surface, what should i do?

To be more clear, I refer you to fig.1 and fig.8
roja:
https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures

Would you please help me how can i reach these goals?

Best regards

Rose
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[gmx-users] Fwd: Difference between gmx spol and gmx h2order in calculationg the orientation of water around surface and solute?

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Sun, 9 Sep 2018, 15:24
Subject: Difference between gmx spol and gmx h2order in calculationg the
orientation of water around surface and solute?
To: 


Hi,

I study the properties of water molecules above surface which is in xy
plane.

I want to calculate the distribution of water polarization above surface. I
didn't do polarizable simulation,  i just mean the orientation of dipole
moment vector if water above surface and calculate the distributios of the
magnitude and y-component of these vectors.

I read about some gmx analyzes but i can't decide that which are really the
best for my needs.

Do you think   gmx spol  can exactly do what i want? So what could be its
difference between gmx h2order in my case? Are they really different in my
case? (As both of them use dipole as water representation)

What about gmx sorient?
If i have an amino acid in my system too, and i wanted to calculate the
orientation of water dipoles around amino acid, should i use gmx spol or
gmx sorient?

I know i asked many questions in one email, but they are really really
important and a little confusing for me. So i really would be appreciated
if you answer  me.

Best rehards

Rose
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[gmx-users] Fwd: How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

-- Forwarded message -
From: rose rahmani 
Date: Mon, 10 Sep 2018, 12:58
Subject: How can i calculate the (ADF)angular distribution of the angles
between water molecule water and surface?
To: Gromacs 


Hi,
How can i calculate the angular distribution of the angles between water
molecule water and surface? surface during molecular dynamics simulation?
 is it possible by GROMACS? gmx gangle?

would you please help me?

To be clear; i refer you to these plots
https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface


Best regards

Rose
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[gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

[rose rahmani]

Hi,
How can i calculate the angular distribution of the angles between water
molecule water and surface? surface during molecular dynamics simulation?
 is it possible by GROMACS? gmx gangle?

would you please help me?

To be clear; i refer you to these plots
https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface


Best regards

Rose
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Re: [gmx-users] Gmx gangle

[rose rahmani]

Is sth wrong or unclear in my question?


On Sun, 9 Sep 2018, 15:01 rose rahmani,  wrote:

> Sorry,
> BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .
>
> How should i define the surface plane?
>
> On Sun, 9 Sep 2018, 14:45 rose rahmani,  wrote:
>
>> Hi,
>>
>> I want to calculate angle between water molecules and ZnS surface(slab).
>> I mean the angular distribution function(ADF) of ALPHA and BETA. I define
>> to angles; Alpha= angle between OH bond of water and  surface(plane)
>> Beta= angle between HOH plane and surface(plane).
>>
>> I used gmax gangle for Alpha:
>> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
>> Then i selected water(SOL) group
>>
>> For Beta:
>> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
>> And again i selected water group.
>>
>> But results are little odd and histograms are two plot which are
>> symmetric plots.
>>
>> I think sth is wrong. Should i make an index file for OH bond in the case
>> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
>> calculated the angle between COM of water vector and surface not the OH
>> bond of water. As you know water has 2 OH bond. So... what should i do?
>>
>> How about BETA? does it really calculate what i want?
>>
>> Should i make an special index file?
>>
>> If i want to calculate this property (ADF) in for example 1 nm from
>> surface, what should i do?
>>
>> To be more clear, I refer you to fig.1 and fig.8
>> roja:
>>
>> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures
>>
>> Would you please help me how can i reach these goals?
>>
>> Best regards
>>
>> Rose
>>
>>
>>
>>
>>
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[gmx-users] Difference between gmx spol and gmx h2order in calculationg the orientation of water around surface and solute?

[rose rahmani]

Hi,

I study the properties of water molecules above surface which is in xy
plane.

I want to calculate the distribution of water polarization above surface. I
didn't do polarizable simulation,  i just mean the orientation of dipole
moment vector if water above surface and calculate the distributios of the
magnitude and y-component of these vectors.

I read about some gmx analyzes but i can't decide that which are really the
best for my needs.

Do you think   gmx spol  can exactly do what i want? So what could be its
difference between gmx h2order in my case? Are they really different in my
case? (As both of them use dipole as water representation)

What about gmx sorient?
If i have an amino acid in my system too, and i wanted to calculate the
orientation of water dipoles around amino acid, should i use gmx spol or
gmx sorient?

I know i asked many questions in one email, but they are really really
important and a little confusing for me. So i really would be appreciated
if you answer  me.

Best rehards

Rose
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Re: [gmx-users] Gmx gangle

[rose rahmani]

Sorry,
BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .

How should i define the surface plane?

On Sun, 9 Sep 2018, 14:45 rose rahmani,  wrote:

> Hi,
>
> I want to calculate angle between water molecules and ZnS surface(slab). I
> mean the angular distribution function(ADF) of ALPHA and BETA. I define to
> angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
> angle between HOH plane and surface(plane).
>
> I used gmax gangle for Alpha:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
> Then i selected water(SOL) group
>
> For Beta:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
> And again i selected water group.
>
> But results are little odd and histograms are two plot which are symmetric
> plots.
>
> I think sth is wrong. Should i make an index file for OH bond in the case
> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
> calculated the angle between COM of water vector and surface not the OH
> bond of water. As you know water has 2 OH bond. So... what should i do?
>
> How about BETA? does it really calculate what i want?
>
> Should i make an special index file?
>
> If i want to calculate this property (ADF) in for example 1 nm from
> surface, what should i do?
>
> To be more clear, I refer you to fig.1 and fig.8
> roja:
>
> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures
>
> Would you please help me how can i reach these goals?
>
> Best regards
>
> Rose
>
>
>
>
>
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[gmx-users] Gmx gangle

[rose rahmani]

Hi,

I want to calculate angle between water molecules and ZnS surface(slab). I
mean the angular distribution function(ADF) of ALPHA and BETA. I define to
angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
angle between HOH plane and surface(plane).

I used gmax gangle for Alpha:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
Then i selected water(SOL) group

For Beta:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
And again i selected water group.

But results are little odd and histograms are two plot which are symmetric
plots.

I think sth is wrong. Should i make an index file for OH bond in the case
of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
calculated the angle between COM of water vector and surface not the OH
bond of water. As you know water has 2 OH bond. So... what should i do?

How about BETA? does it really calculate what i want?

Should i make an special index file?

If i want to calculate this property (ADF) in for example 1 nm from
surface, what should i do?

To be more clear, I refer you to fig.1 and fig.8
roja:
https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures

Would you please help me how can i reach these goals?

Best regards

Rose
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[gmx-users] Make_ndx for gmx hbond

[rose rahmani]

Hi,

I want yo do gmx hbond analysis. I have an capped tyrosine amino acid in a
box of water. I want to calculate number of hydrogen bonds that amino acid
make with the waters around it. But i couldn't understand the manual
description about how make an index file for this purpose. If i choose
group protein and sol in make_ndx command does it give me what i want? Or i
should specify the O and N atoms in amino acid and make index for it
seperately? If yes, i couldn't understand how to choose an atom from the
help which comes with make_ndx command( should i write
atom type O
atom type N )?

Would you please help me? I couldn't understand the manual.

Best regards
Rose
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[gmx-users] Water properties above surface

[rose rahmani]

Hi,

I study the interaction of different amino acid above surface in presence
of (TIP3P)water in physiological ion concentration(150mM) and i calculated
PMF for different distances of AA above surface.
Now, i want to find different proofs which prove the importance of water
molecules, amino acids different polarities and hydrophobicities and water
layer formed above surface in the quality of AA interaction with surface.
I searched about every tools in lovely GROMACS to calculate these
properties; So,

1- We all know about different amino acids properties(polarity,
hydrophobicity, ...) generally, but i could not find any tool in GROMACS to
quantitively prove these properties (amino acids) in different systems.
However i think it is not possible at all;) , we should search about
different clues,... . for example i want to show the distribution of water
in RADIAL distances around AA  to show the hydrophobicity/phility but i
don't know which tool can do it? is gmx spol appropeiate for these goals?
( I will refer you to these question's attached filehttps://
www.researchgate.net/post/How_can_i_calculate_the_distribution_of_water_polarization_above_surface
)

2- number density profile of water above surface which causes forming
solvent layers... fortunately i could do it by gmx density. but how about
the orientation of water molecules near the surface? how can i show that?
can gmx hydorder or gmx sorient does?
3- and what i have never understand about gmx SASA is that; for example
when i choose protein and SOL group, what does it exactly calculate? does
it will calculate the solvent area around AA??

sorry for multiple question
I would be grateful if you answer to them.

Best regards

Rose
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Re: [gmx-users] Qm/mm

[rose rahmani]

Hi Albert,

I want to study the interaction of functionalized inorganic nanotube with
protein. I just can use free software. Is ORCA ok for my needs? I don't
know anything about it.i couldn't use some softwares like Gaussian and
quantum espresso because Gaussian is commercial and Quantum Espresso is not
Ok for nanotube with more than 100 atoms...
Is ORCA suitable for these systems?[ Does it need special computers(high
processing)? I use computer (linux)with RAM 32GB]
If yes, would you please introduce me some valuable sites and tutorials for
ORCA BEGINNER users?

Best

Rose

On Sat, 25 Aug 2018, 18:18 Albert,  wrote:

> why not try some professional QM/MM software like "ORCA". It will make
> your life much easier.
>
>
> On 08/24/2018 11:54 PM, rose rahmani wrote:
> > Hi,
> >
> > I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs.
> > Since, some of these codes are commercial(like ONIOM specially
> Gaussian), i
> > wanted to ask are these all free in GROMACS? Or we should first register
> > and by these codes separately and then use them in GROMACS?
> >
> > Best regards
> >
> > Rose
>
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Re: [gmx-users] Qm/mm

[rose rahmani]

Sorry, what you mean exactly? You mean other free softwares or GROMACS?

On Sat, 25 Aug 2018, 02:28 Benson Muite,  wrote:

> I believe for the non free codes, you would need to obtain a license.
> Depending on the calculation you want to do, there are free alternatives
> to the non free codes.
>
>
> On 08/25/2018 12:54 AM, rose rahmani wrote:
> > Hi,
> >
> > I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs.
> > Since, some of these codes are commercial(like ONIOM specially
> Gaussian), i
> > wanted to ask are these all free in GROMACS? Or we should first register
> > and by these codes separately and then use them in GROMACS?
> >
> > Best regards
> >
> > Rose
>
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[gmx-users] Qm/mm

[rose rahmani]

Hi,

I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs.
Since, some of these codes are commercial(like ONIOM specially Gaussian), i
wanted to ask are these all free in GROMACS? Or we should first register
and by these codes separately and then use them in GROMACS?

Best regards

Rose
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Re: [gmx-users] Qmmm (rose rahmani) (Rose)

[rose rahmani]

Thank you so much.

On Mon, 6 Aug 2018, 23:50 Groenhof, Gerrit,  wrote:

>
> I live in iran and we don't access to Gaussian.
> You think DFTB3 (maybe)could be better choice as it's free?
>
> As I wrote earlier, that depends on whether DFTB3 provides a sufficiently
> accurate description for your system. To find that out you need to either
> perform a series of benchmarks, or go through the literature in which the
> methods has been used successfully for similar systems.
>
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Re: [gmx-users] Qmmm (rose rahmani)

[rose rahmani]

Thank you so mich for your derailed answer.

On Mon, 6 Aug 2018, 00:04 Groenhof, Gerrit,  wrote:

> Hi,
>
> What is exactly your question?
>
> If it is whether you can use gromacs for QM/MM, the answer is yes.
>
> Whether your QM/MM model it is valid, is always up to you to check, as
> with any other pure QM, MM or QM/MM model. Sometimes, the validation for
> the model can be found in literature, sometimes you need to do a careful
> benchmark yourself.
>
> If for your systems,  DFTB is a valid model, then I can recommend using
> the DFTB implementation. If not, and you need ab initio or DFT  models,
> then you'd have to resort to a QM program that supports these methods for
> the QM engine in your QM/MM simulations. In that case, you can use the gau
> script from http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian

Is it free to use Gaussian?( as it's not free software generally)

>
> Gerrit
>
>
>
>
> Hi,
>
> I want to study the interaction of protein with functionalized
> nanotube(different fuctional groups) to know how protein can bind to
> functionalizedNT and calculate binding affinity,... . I want to try QMMM
> implemention in gromacs but as i'm beginner in such calculation methods(in
> gromacs), i wanna know am i right in using such method in GROMACS. Is ONIOM
> method and dft calculations just like quantum base softwares ( like
> Gaussian,...) ? I use to do MD simulations by GROMACS and results were
> always great but i have not tried QMMM. Is it as valid as quantum base
> calculation softwares?(sorry for being rude ;)))
> And how about this one
>
> http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
> ?is
> 
> it recommended by GROMACS developers?
>
> Best regards
> Rose
>
>
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[gmx-users] Qmmm

[rose rahmani]

Hi,

I want to study the interaction of protein with functionalized
nanotube(different fuctional groups) to know how protein can bind to
functionalizedNT and calculate binding affinity,... . I want to try QMMM
implemention in gromacs but as i'm beginner in such calculation methods(in
gromacs), i wanna know am i right in using such method in GROMACS. Is ONIOM
method and dft calculations just like quantum base softwares ( like
Gaussian,...) ? I use to do MD simulations by GROMACS and results were
always great but i have not tried QMMM. Is it as valid as quantum base
calculation softwares?(sorry for being rude ;)))
And how about this one
http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
?is it recommended by GROMACS developers?

Best regards
Rose
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[gmx-users] Umbrella sampling

[rose rahmani]

Hi,

I do umbrella sampling for different distances of AA along surface and i
calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1
in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2
kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows
overlapped in histo plot.
So how should i know that this error is neglectable or not? I did sampling
many times but near surface, the error is too much and windows have
significant overlapping and count is about 2 times higher than 0.8 to 1.7
nm.
Would you please help me? Is there any criteria other than overlapping and
estimating error i should notice to?
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[gmx-users] Umbrella saming

[rose rahmani]

I do umbrella sampling for different distances of AA perpendicular to
nanotube axis. Imagine nanotube is along Y axis and i want to pull AA along
just Z axis. But during pulling (i mean most of the time) it trapped in X
axis and pulls along x axis.
I used pull_vec= 0 0 1 and pull_geometry= direction, force constant= 5000 .
How can i make it to move just along Z axis?
Would you please help me?

Best regards
-Rose
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Re: [gmx-users] Position restrain in umbrella sampling

[rose rahmani]

I checked it for each window. it just oscillates just for 0.1nm in each
window and results are ok.
I just asked to realize your main purpose ...
And i'm convinced now ;) .
Thank you for your kindly and detailed answers like always.

Best regards
-Rose

On Wed, 6 Jun 2018, 20:01 Justin Lemkul,  wrote:

>
>
> On 6/6/18 11:18 AM, rose rahmani wrote:
> > Hi,
> >
> > I'm doing umbrella sampling for different distances of amino acid from
> > surface.
> > I know that dear Justin warns people that position restraint was for that
> > specific situation in the article mentioned in tutorial and 
> > I know it doesn't make a sense in my system too in PULLING. But i don't
> > understand why it's not usable for the rest; i mean in nvt_umbrella for
> > each window and conformation. I extract different conformations to show
> the
> > potential of mean force on that exact distance. So if i don't use
> position
> > restraint for AA in for example 0.5nm distance from surface so i can't
> > claim that this nvt_umbrella run is showing the system manner in a
> > situation that AA is about 0.5 from surface because without position
> > restraint(for AA) the AA can be anywhere in box ... . ( i should mention
> > that surface is frozen in my system)Would you please correct me if i'm
> > wrong?
>
> You shouldn't be layering biases upon biases to try to force a certain
> behavior. It is possible to combine various restraints as long as the
> resulting PMF is corrected for these effects.
>
> For each window, you define an origin of the umbrella potential. If
> that's 0.5 nm and the specified COM distance (or whatever) does not
> oscillate about this value, then there are two possibilities: (1) Your
> force constant is not large enough or (2) the physical forces in your
> system are such that it is not physically reasonable for the entities to
> exist at that interaction distance.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Position restrain in umbrella sampling

[rose rahmani]

Hi,

I'm doing umbrella sampling for different distances of amino acid from
surface.
I know that dear Justin warns people that position restraint was for that
specific situation in the article mentioned in tutorial and 
I know it doesn't make a sense in my system too in PULLING. But i don't
understand why it's not usable for the rest; i mean in nvt_umbrella for
each window and conformation. I extract different conformations to show the
potential of mean force on that exact distance. So if i don't use position
restraint for AA in for example 0.5nm distance from surface so i can't
claim that this nvt_umbrella run is showing the system manner in a
situation that AA is about 0.5 from surface because without position
restraint(for AA) the AA can be anywhere in box ... . ( i should mention
that surface is frozen in my system)Would you please correct me if i'm
wrong?

Best regards
-Rose
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Re: [gmx-users] Box dimension

[rose rahmani]

Is there any suggestion about how can i make this system in least box size?
with periodic boundary condition in all dimensions?put NT in middle or at
z=0?

Best
-Rose

On Mon, Jun 4, 2018 at 2:19 PM, rose rahmani  wrote:

> It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
> for optimization and obtaining charges.  I did this job for an slab before.
> I mean the AA was between slab surface and wall but it was the vaccum space
> before slab and after wall. imagine this structures in a box of z=12. The
> slab was in z=4 and wall in z=7.5 and WATER between z=4 to7.5  So z=0
> to 4 and 7.5 to 12 is in vaccum. and AA is between z=4 to 7.5 .
> I think it's clear now.
>
> Best regards
> -Rose
>
> On Mon, 4 Jun 2018, 13:37 Alex,  wrote:
>
>> It's a bit unclear what's happening in your system. Are you simulating
>> in vacuum, or in solvent? I am assuming it's in solvent and that the
>> word "vacuum" simply means space unoccupied by the structure, i.e. a
>> term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
>> forms various interfaces at the boundary, so simply look at the
>> interface data and/or other literature and see roughly how much space is
>> needed to accommodate that in addition to everything else.
>>
>> Yes, people do put their NTs between walls with a periodic boundary,
>> which requires that the nanotube edges are crystallographically
>> periodic, i.e. fits a supercell. It is a very useful practice.
>>
>> Alex
>>
>>
>> On 6/4/2018 2:48 AM, rose rahmani wrote:
>> > Sorry i should correct myself
>> >
>> > On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:
>> >
>> >> I have nothing to say...
>> >> but i'm a beginner and i comment here to have your ideas as
>> experienced.
>> >>   It's not CNT. It's an inorganic nanotube which its partial atomic
>> charges
>> >> (0.48 , -0.48) is calculated by DFT.
>> >>
>> >> When i optimized structure in other packages i put it in box with Z=3.
>> So
>> >> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
>> >> z=2.15 and the "COM" is in z=1.5 .
>> >> So NT outer curvature which is in touch with AA is in z=2.15(0.85 +
>> 1.3)
>> >> Did you calculate these arithmetics when the z dimension of CNT started
>> >> from z=0 to z=1.3?
>> >>
>> >> People sometimes put NT between 2 walls? As the z=7 need much more
>> water
>> >> and long calculations. Do you think put NT between two walls and use
>> vaccum
>> >>
>> > Use box 3times distances between two walls so the vaccum is 2/3 this
>> > distance
>> >
>> >> 3times distances between walls is better
>> >>
>> > than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 +
>> thickness
>> >> of two walls) how do you think, sir?
>> >>
>> >> With regards
>> >> -Rose
>> >>
>> >>
>> >>
>> >>
>> >> On 4 Jun 2018 12:04, "Alex"  wrote:
>> >>
>> >> I'm kind and civil, practically a sweetheart. I just can't put smiley
>> >> faces everywhere! On the other hand, it does not hurt to try things and
>> >> have a little bit of initiative. I don't know why I am telling you
>> this,
>> >> like you've never supervised students... Also, CNTs are simulated
>> >> exactly the same way (within these forcefield flavors) as pretty much
>> >> anything else you can think of. That is, until one day when you guys
>> >> decide to come with a testing Gromacs version that includes FFs not
>> >> relying on permanent topologies. ;)
>> >>
>> >>
>> >> Alex
>> >>
>> >>
>> >>
>> >> On 6/4/2018 1:28 AM, Mark Abraham wrote:
>> >>> Hi,
>> >>>
>> >>> Let's keep the discussion kind and civil, please. What's obvious when
>> you
>> >>> have experience often isn't when you are new. :-) I sure don't
>> understand
>> >>> the arithmetic involved, but then I've never attempted a CNT
>> simulation!
>> >>>
>> >>> Mark
>> >>>
>> >>> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
>> >>>
>> >>>> And again, your question has nothing to do with Gromacs. It has to do
>> >>>> with what you want to do, common sense, and basic arithmetic.
>> >&

Re: [gmx-users] Box dimension

[rose rahmani]

It's ZnS and yes it's periodic and in water not in vaccum. I used DFT just
for optimization and obtaining charges.  I did this job for an slab before.
I mean the AA was between slab surface and wall but it was the vaccum space
before slab and after wall. imagine this structures in a box of z=12. The
slab was in z=4 and wall in z=7.5 and WATER between z=4 to7.5  So z=0
to 4 and 7.5 to 12 is in vaccum. and AA is between z=4 to 7.5 .
I think it's clear now.

Best regards
-Rose

On Mon, 4 Jun 2018, 13:37 Alex,  wrote:

> It's a bit unclear what's happening in your system. Are you simulating
> in vacuum, or in solvent? I am assuming it's in solvent and that the
> word "vacuum" simply means space unoccupied by the structure, i.e. a
> term used by DFT folks. With all nanotubes (carbon, ZnS, BN, etc), water
> forms various interfaces at the boundary, so simply look at the
> interface data and/or other literature and see roughly how much space is
> needed to accommodate that in addition to everything else.
>
> Yes, people do put their NTs between walls with a periodic boundary,
> which requires that the nanotube edges are crystallographically
> periodic, i.e. fits a supercell. It is a very useful practice.
>
> Alex
>
>
> On 6/4/2018 2:48 AM, rose rahmani wrote:
> > Sorry i should correct myself
> >
> > On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:
> >
> >> I have nothing to say...
> >> but i'm a beginner and i comment here to have your ideas as experienced.
> >>   It's not CNT. It's an inorganic nanotube which its partial atomic
> charges
> >> (0.48 , -0.48) is calculated by DFT.
> >>
> >> When i optimized structure in other packages i put it in box with Z=3.
> So
> >> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
> >> z=2.15 and the "COM" is in z=1.5 .
> >> So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
> >> Did you calculate these arithmetics when the z dimension of CNT started
> >> from z=0 to z=1.3?
> >>
> >> People sometimes put NT between 2 walls? As the z=7 need much more water
> >> and long calculations. Do you think put NT between two walls and use
> vaccum
> >>
> > Use box 3times distances between two walls so the vaccum is 2/3 this
> > distance
> >
> >> 3times distances between walls is better
> >>
> > than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 +
> thickness
> >> of two walls) how do you think, sir?
> >>
> >> With regards
> >> -Rose
> >>
> >>
> >>
> >>
> >> On 4 Jun 2018 12:04, "Alex"  wrote:
> >>
> >> I'm kind and civil, practically a sweetheart. I just can't put smiley
> >> faces everywhere! On the other hand, it does not hurt to try things and
> >> have a little bit of initiative. I don't know why I am telling you this,
> >> like you've never supervised students... Also, CNTs are simulated
> >> exactly the same way (within these forcefield flavors) as pretty much
> >> anything else you can think of. That is, until one day when you guys
> >> decide to come with a testing Gromacs version that includes FFs not
> >> relying on permanent topologies. ;)
> >>
> >>
> >> Alex
> >>
> >>
> >>
> >> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> >>> Hi,
> >>>
> >>> Let's keep the discussion kind and civil, please. What's obvious when
> you
> >>> have experience often isn't when you are new. :-) I sure don't
> understand
> >>> the arithmetic involved, but then I've never attempted a CNT
> simulation!
> >>>
> >>> Mark
> >>>
> >>> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
> >>>
> >>>> And again, your question has nothing to do with Gromacs. It has to do
> >>>> with what you want to do, common sense, and basic arithmetic.
> >>>>
> >>>> CNTs interact at pretty short range (if they are intact and without
> edge
> >>>> passivation), so I'd just go with a distance sweep range of ~1.5 nm
> and
> >>>> give it some additional space, say, 1 nm, and finally keep the box
> >>>> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1)
> x
> >>>> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> >>>> shorten the box.
> >>>>
> >>>> Alex
> >>>>
> >>>>
> >>>> On 6/4/2018 12:53 AM, ro

Re: [gmx-users] Box dimension

[rose rahmani]

Sorry i should correct myself

On Mon, 4 Jun 2018, 13:10 rose rahmani,  wrote:

> I have nothing to say...
> but i'm a beginner and i comment here to have your ideas as experienced.
>  It's not CNT. It's an inorganic nanotube which its partial atomic charges
> (0.48 , -0.48) is calculated by DFT.
>
> When i optimized structure in other packages i put it in box with Z=3. So
> first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
> z=2.15 and the "COM" is in z=1.5 .
> So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
> Did you calculate these arithmetics when the z dimension of CNT started
> from z=0 to z=1.3?
>
> People sometimes put NT between 2 walls? As the z=7 need much more water
> and long calculations. Do you think put NT between two walls and use vaccum
>
Use box 3times distances between two walls so the vaccum is 2/3 this
distance

> 3times distances between walls is better
>
than multiply 2 to keep it symmetric?(now you have 1.3 + 2*1.5 + thickness
> of two walls) how do you think, sir?
>
> With regards
> -Rose
>
>
>
>
> On 4 Jun 2018 12:04, "Alex"  wrote:
>
> I'm kind and civil, practically a sweetheart. I just can't put smiley
> faces everywhere! On the other hand, it does not hurt to try things and
> have a little bit of initiative. I don't know why I am telling you this,
> like you've never supervised students... Also, CNTs are simulated
> exactly the same way (within these forcefield flavors) as pretty much
> anything else you can think of. That is, until one day when you guys
> decide to come with a testing Gromacs version that includes FFs not
> relying on permanent topologies. ;)
>
>
> Alex
>
>
>
> On 6/4/2018 1:28 AM, Mark Abraham wrote:
> > Hi,
> >
> > Let's keep the discussion kind and civil, please. What's obvious when you
> > have experience often isn't when you are new. :-) I sure don't understand
> > the arithmetic involved, but then I've never attempted a CNT simulation!
> >
> > Mark
> >
> > On Mon, Jun 4, 2018, 09:08 Alex  wrote:
> >
> >> And again, your question has nothing to do with Gromacs. It has to do
> >> with what you want to do, common sense, and basic arithmetic.
> >>
> >> CNTs interact at pretty short range (if they are intact and without edge
> >> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
> >> give it some additional space, say, 1 nm, and finally keep the box
> >> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
> >> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
> >> shorten the box.
> >>
> >> Alex
> >>
> >>
> >> On 6/4/2018 12:53 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to do umbrella sampling for different coordination of amino acid
> >>> through different distances (in Z dimension) from nanotube. The
> nanotube
> >>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
> >>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
> >>> (because the nanotube radius is 0.65nm). The initial distance of amino
> >> acid
> >>> from nanotube is 2nm. The question is how should i choose the box Z
> >>> dimension that some artifacts (justin explained in tutorial) doesn't
> >>> happen? I choose 7nm, is it ok or large?
> >>>
> >>> Would you please help me?
> >>>
> >>> Best regards
> >>> -Rose
> >> --
> >> 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] Box dimension

[rose rahmani]

I have nothing to say...
but i'm a beginner and i comment here to have your ideas as experienced.
 It's not CNT. It's an inorganic nanotube which its partial atomic charges
(0.48 , -0.48) is calculated by DFT.

When i optimized structure in other packages i put it in box with Z=3. So
first i have box Z=3 it means z dimension of nanotube is in z=0.85 to
z=2.15 and the "COM" is in z=1.5 .
So NT outer curvature which is in touch with AA is in z=2.15(0.85 + 1.3)
Did you calculate these arithmetics when the z dimension of CNT started
from z=0 to z=1.3?

People sometimes put NT between 2 walls? As the z=7 need much more water
and long calculations. Do you think put NT between two walls and use vaccum
3times distances between walls is better than multiply 2 to keep it
symmetric?(now you have 1.3 + 2*1.5 + thickness of two walls) how do you
think, sir?

With regards
-Rose




On 4 Jun 2018 12:04, "Alex"  wrote:

I'm kind and civil, practically a sweetheart. I just can't put smiley
faces everywhere! On the other hand, it does not hurt to try things and
have a little bit of initiative. I don't know why I am telling you this,
like you've never supervised students... Also, CNTs are simulated
exactly the same way (within these forcefield flavors) as pretty much
anything else you can think of. That is, until one day when you guys
decide to come with a testing Gromacs version that includes FFs not
relying on permanent topologies. ;)


Alex



On 6/4/2018 1:28 AM, Mark Abraham wrote:
> Hi,
>
> Let's keep the discussion kind and civil, please. What's obvious when you
> have experience often isn't when you are new. :-) I sure don't understand
> the arithmetic involved, but then I've never attempted a CNT simulation!
>
> Mark
>
> On Mon, Jun 4, 2018, 09:08 Alex  wrote:
>
>> And again, your question has nothing to do with Gromacs. It has to do
>> with what you want to do, common sense, and basic arithmetic.
>>
>> CNTs interact at pretty short range (if they are intact and without edge
>> passivation), so I'd just go with a distance sweep range of ~1.5 nm and
>> give it some additional space, say, 1 nm, and finally keep the box
>> symmetric. With CNT diameter of 1.3 nm, this would be (1.3 + 1.5 + 1) x
>> 2 = 7.6 nm. You could of course place the CNT off center (in Z) to
>> shorten the box.
>>
>> Alex
>>
>>
>> On 6/4/2018 12:53 AM, rose rahmani wrote:
>>> Hi,
>>>
>>> I want to do umbrella sampling for different coordination of amino acid
>>> through different distances (in Z dimension) from nanotube. The nanotube
>>> axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
>>> curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
>>> (because the nanotube radius is 0.65nm). The initial distance of amino
>> acid
>>> from nanotube is 2nm. The question is how should i choose the box Z
>>> dimension that some artifacts (justin explained in tutorial) doesn't
>>> happen? I choose 7nm, is it ok or large?
>>>
>>> Would you please help me?
>>>
>>> Best regards
>>> -Rose
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>>

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[gmx-users] Box dimension

[rose rahmani]

Hi,

I want to do umbrella sampling for different coordination of amino acid
through different distances (in Z dimension) from nanotube. The nanotube
axis is along X axis. The COM of nanotube is in Z=1.5 and its outer
curvature(which is in touch with amino acid) is in Z=1.5 +0.65=2.15
(because the nanotube radius is 0.65nm). The initial distance of amino acid
from nanotube is 2nm. The question is how should i choose the box Z
dimension that some artifacts (justin explained in tutorial) doesn't
happen? I choose 7nm, is it ok or large?

Would you please help me?

Best regards
-Rose
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[gmx-users] Partial charges

[rose rahmani]

Hi,

I used QM for calculating atoms partial charges for ZnS nanotube but it has
totally -0.04 charge. I want to study the interaction of this nanotube with
some biomolecules by AMBER99SB force field.
Is it wrong to calculate these interaction in presence of -0.04 charge by
this force field? Should i neglect it?
Would you please help me or give me a suggestion?

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[gmx-users] Purpose of using (reflecting) WALL in MD simulations?

[rose rahmani]

Hi,

Thre are some articles which use (reflecting)walls(for example carbon
walls) in simulation of nanosheet and nanotubes. But i didn't understand
the main purpose of using walls in simulation; specially in the case of an
infinite nanotube (or nanosheet). Why NPT simulation couldn't be done in
these situations?

Can anyone tell me the purpose and advantage of this modeling?

Regards
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[gmx-users] S-S bond

[rose rahmani]

Hi,

I want to functionalize ZnS  nanotube with different molecules which all
have sulfur in their structures, like cystein amino acid and ... . I want
to study the interaction of  this functionalized nanotube with different
proteins.

I use DFT  for calculating the partial charges and bond length in ZnS
nanotube and made an .itp file for it.

If i know that cystein (and all those molecules) can BIND to ZnS with their
sulfur atom, can AMBER define this this S(from cystein)-S(from ZnS
nanotube) bond? Is this special S-S bond like that S-S which is in amber?
There is an article which correspond to interaction of ZnS with cystein by
umbrella sampling. In this article the binding energy and bond length in
minimum PMF is calculated. How about this bond length? It couldn't be used
as S-S bond length for ZnS nanotube cystein?

Is it better to use DFTcalculation for all these structures and just do
functionalized nanotube with protein by AMBER force field?

Could you please help me?

Best regards
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Re: [gmx-users] mdrun error

[rose rahmani]

!!!
I have sheet(at z=0) and 2wall(are close to each other and one of them
begins at z=3.5 and the other at z=~3.8) structures which the other
molecules(water, AA, NA, CL) are BETWEEN sheet and wall structures. before
solvation, i add box size without considering the wall in coordination
because i didn't want that sol molecules enter the space between two carbon
WALLs. After solvation in EM step because of PBC issues i had to increase
the box size in x dimension for 0.094 nm. The box size in z dimension is
almost 3times bigger than the distance between walls and sheet ( box
size=12 nm) because of PBC.

I try to figure out what happens and please correct me if i am wrong;
1, as i can see in .gro file 3 water molecules are in vaccum space so may
feel larger force.

2, some water molecules are between to carbon walls(maybe they could get
there because of 0.094nm space that i added to x dimension)

3, number of water molecules is not enough for this size of system.

4, i know that the system in energy minimization (before pulling) minimized
with minus Kj/mol and didn't fluctuate, but GROMACS said in didn't get
converged.

5, i constraint hbonds and because of that i decided to choose dt=2fs. As
far as i know hbonds have the highest vibrational frequency and least
time so i choose 2fs...

Could you please help me which one caused to problem?

Regards
-Rose

On Tue, 22 May 2018, 01:19 Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 5/21/18 4:47 PM, rose rahmani wrote:
> > Hi,
> >
> > I do umbrella sampling with GROMACS4.5.4 version. I got this error
> > "A charge group moved too far between two domain decomposition steps."
> > But when i try it in another computer(version 4.5.4 was also installed
> > there) this error doesn't exist any more! How could it be possible?which
> > one is correct?
>
> Welcome to the stochastic nature of MD. You have an unstable system that
> occasionally works. Don't trust it - figure out where the instability
> comes from and/or prepare the system more gently.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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[gmx-users] mdrun error

[rose rahmani]

Hi,

I do umbrella sampling with GROMACS4.5.4 version. I got this error
"A charge group moved too far between two domain decomposition steps."
But when i try it in another computer(version 4.5.4 was also installed
there) this error doesn't exist any more! How could it be possible?which
one is correct?

Best
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[gmx-users] Partial charges calculation

[rose rahmani]

Hi,

I want to calculate partial charges for nanotube capped with amino acid. I
use DFT calculation when it is just nano tube with out any amino acid. As
far as i know the amino acid partial charges for AA in amber99 are
calculated by
HF/6-31G* RESP calculation.
The question is that, if i use DFT calculation for optimizing and
calculating partial charges for nanotube- amino acid system, would amino
acid partial charges be wrong or overstimated? I want to use this
structures an an input(.itp file) for MD simulations in GROMACS  using
amber99 ff.

Best regards
-Rose
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[gmx-users] Gmx insert

[rose rahmani]

Hi,

I want to place peptide at certain distance from surface as an initial
distance. How can i do it? Is it possible with gmx insert molecule?

Best regards
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Re: [gmx-users] Distribution of water polarization

[rose rahmani]

On Fri, 11 May 2018, 20:04 Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 5/11/18 11:29 AM, rose rahmani wrote:
> > On Fri, 11 May 2018, 19:38 Justin Lemkul, <jalem...@vt.edu> wrote:
> >
> >>
> >> On 5/11/18 11:06 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> How can i calculate the distribution of water polarization for example
> >> for
> >>> the first two layers of water at the solid surface?
> >>>
> >>> How about the number of water molecules with a given polarization?
> >>>
> >>> I mean exactly figure2 of this article.
> >>> Can gmx dipoles do it?
> >> Did you do a polarizable simulation?
> >>
> > No, it is sth like calculating the distribution of polarization (dipole)
> in
> > different dimensions separately. Sth like different orientation of water
> > molecules which cause to different orientations of dipoles in different
> > dimensions. (Hope to explain clearly, if it's possible please take a look
> > at the article)
>
> There is no article, nothing linked, but in

Sorry, i forgot to send it. The figure 2

https://aip.scitation.org/doi/abs/10.1063/1.4866763?journalCode=jcp

any case I'm not going to
> have time to look into it.
>
Ok, but i sent... It maybe useful for someone. ;)

> If you've done a classical, nonpolarizable MD simulation, you can make
> no claims about polarization. You could compute properties related to
> water molecule orientation (e.g. gmx hydorder), which will tell you
> about the dipole moment orientation in the context of a fixed triangle
> of charges, but that's all you're going to get from simulations like
> these. FWIW, in reality, the dipole moment of the water molecules will
> not be exactly related to these fixed geometries, so this is a weak
> comparison, in my mind.
>
Thank you so much for your detailed answer.

> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Distribution of water polarization

[rose rahmani]

On Fri, 11 May 2018, 19:38 Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 5/11/18 11:06 AM, rose rahmani wrote:
> > Hi,
> >
> > How can i calculate the distribution of water polarization for example
> for
> > the first two layers of water at the solid surface?
> >
> > How about the number of water molecules with a given polarization?
> >
> > I mean exactly figure2 of this article.
> > Can gmx dipoles do it?
>
> Did you do a polarizable simulation?
>
No, it is sth like calculating the distribution of polarization (dipole) in
different dimensions separately. Sth like different orientation of water
molecules which cause to different orientations of dipoles in different
dimensions. (Hope to explain clearly, if it's possible please take a look
at the article)

> Rigid, fixed-charge water molecules all have identical dipole moments,
> by definition.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Distribution of water polarization

[rose rahmani]

Hi,

How can i calculate the distribution of water polarization for example for
the first two layers of water at the solid surface?

How about the number of water molecules with a given polarization?

I mean exactly figure2 of this article.
Can gmx dipoles do it?


Best regards
-Rose
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Re: [gmx-users] Helical structure .itp file

[rose rahmani]

Thank you somuch. I build it with anoyher software(Peptide buikder). But
can i add NME and ACE terminals by GROMACS?

On Mon, 7 May 2018, 19:46 Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 5/7/18 11:14 AM, rose rahmani wrote:
> > Hi ,
> >
> > I want to build poly amino acids like poly threonine(ACE THR THR ... NME)
> > BUT in its helical structure which its topology file is compatible with
> > amber forcefield in GROMACS. Is there any way to build this structure in
> > GROMACS?
>
> GROMACS has no ability to construct molecules.
>
> > Would you please help me?
>
> Use Leap in AMBER.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Box size

[rose rahmani]

Hi,

I have two nanosheet structure and they are infront of each other and about
3 nm far from each other.
I have some problems in fitting the box size. I used many options
triclinic, -box,... to fit the size, but it's not possible. The problem is
that atoms in ZnS nanosheet are not aligned and are up & down and this
makes the minus z dimension coordination and i can't use -box option. How
can i solve this problem? I want to make box size as fit as possible to
have the least solvent molecules in next step.

Regards
-Roja
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[gmx-users] Helical structure .itp file

[rose rahmani]

Hi ,

I want to build poly amino acids like poly threonine(ACE THR THR ... NME)
BUT in its helical structure which its topology file is compatible with
amber forcefield in GROMACS. Is there any way to build this structure in
GROMACS?
Would you please help me?


Best regards
-Rose
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[gmx-users] Topology file for amino acid

[rose rahmani]

Hi,

 I want to add NME and ACE terminals to zwitterionic amino acid like
threonine and then make an input topology file for GROMACS(.itp file) to be
compatible with (AMBER99 ff in) GROMACS.

I have tried many tutorials like(
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/) but
everytime i get confused in the middle because they are little different
from my need.
(I ask in AMBER mailing list but there is no answer)

Could you please introduce me straightforward solution or tutorial which is
most simmilar to my needs?

Best regards
-Rose
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[gmx-users] (no subject)

[rose rahmani]

Hi,

I have a capped amino acid in box of water and ion(but the system is not
charged) and named it initial.gro, i can see some unreal bonds when i open
it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H
atom where nonbobded and were single atoms around remained bonded
structure.( maybe aminoacid in initial.gro file didn't get well optimized
or anything... )

But when i run nvt, the amino acid structure get real structure and
everything is ok.

I remember Justin said that MD and GROMACS can't make or break bond. So
What happend to my system?

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Re: [gmx-users] Gmx_solvate

[rose rahmani]

But the box size is 4 4 12 and i should make an index for about 2000 SOL.
Is there any better solution?


On Mon, 16 Apr 2018, 17:34 Justin Lemkul, <jalem...@vt.edu> wrote:

>
>
> On 4/16/18 8:51 AM, rose rahmani wrote:
> > Thank you so much.
> > You mean first use gmx solvate, then delete the Sol molecules which i
> dont
> > need them?
>
> Yes.
>
> > So trjorder can fix the rest, yes?
>
> No, but trjconv can save what you want based on an index group from gmx
> select.
>
> -Justin
>
> > On Mon, 16 Apr 2018, 16:26 Justin Lemkul, <jalem...@vt.edu> wrote:
> >
> >>
> >> On 4/16/18 5:58 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I have input structure from my last simulation. The box is 12nm long
> in Z
> >>> axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8
> >> to
> >>> 12 is empty) .  I want to add solvent between z=3-8. How can i do that?
> >>> The problem is that i cant adjust wall and sheet( z coordination) to
> >> start
> >>> from z=0 of box.
> >>> I mean when i extract wall and sheet from my last simulation and open
> it
> >> in
> >>> a viewer they wont start from 0, which is not odd. So i cant use the
> box
> >>> size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
> >>> larger.
> >>> What is your idea? Is there any tool to add solvate in specific
> >> dimensions?
> >>
> >> No.
> >>
> >>> Would you please help me?
> >> Write a script to remove solvent molecules based on coordinates, or use
> >> gmx select write an index group to do the same.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> Gromacs Users mailing list
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> >> posting!
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> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
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Re: [gmx-users] Gmx_solvate

[rose rahmani]

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

On Mon, 16 Apr 2018, 16:26 Justin Lemkul, <jalem...@vt.edu> wrote:

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

[rose rahmani]

Hi,

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

Best regards
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Re: [gmx-users] force field parameters for Fe3O4?

[rose rahmani]

Hello,

I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?

Thank you so much

On Fri, 13 Apr 2018, 14:50 Paul bauer, <paul.baue...@gmail.com> wrote:

> Hello,
>
> this depends on the force field you are using. Some of them use
> parameters from a QM optimization and partial charge calculation.
> But even then you need to be careful that the results from the QM are
> not just random numbers :)
>
> But I'm not sure myself how I would tackle something like Magnetite
> right now, as it would also require obtaining parameters for the LJ
> interactions.
>
> Cheers!
>
> On 13/04/18 12:13, rose rahmani wrote:
> > On Fri, 13 Apr 2018, 14:35 Paul bauer, <paul.baue...@gmail.com> wrote:
> >
> >> Hello,
> >>
> >> I would recommend that you check relevant publications for the
> >> simulation of magnetite if people have tried to simulate it in solvent.
> >> I could not find anything during a short search, but maybe you'll be
> >> more successful. :)
> >> If there are no published parameters in the literature you will have to
> >> parametrize the molecule yourself according to the method used by the
> >> force field you are using.
> >> I would look at the section in the user guide dealing with this
> >> (
> >>
> http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields
> )
> >>
> >>
> > Is it true to optimize the molecule for example in gaussian(dft)first,
> and
> > then calculate the charges and make an .itp file for it?is it always
> > reliable?
> >
> >> and then at the documentation for your force field!
> >>
> >> Cheers!
> >>
> >> On 13/04/18 11:21, leila karami wrote:
> >>> Dear gromacs users,
> >>>
> >>> I want to simulate a protein in different concentration of Fe3O4.
> >>>
> >>> How to obtain force field parameters of Fe3O4?
> >>>
> >>> Any help will highly be appreciated.
> >>>
> >>> Best,
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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> >> posting!
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Re: [gmx-users] force field parameters for Fe3O4?

[rose rahmani]

On Fri, 13 Apr 2018, 14:35 Paul bauer,  wrote:

> Hello,
>
> I would recommend that you check relevant publications for the
> simulation of magnetite if people have tried to simulate it in solvent.
> I could not find anything during a short search, but maybe you'll be
> more successful. :)
> If there are no published parameters in the literature you will have to
> parametrize the molecule yourself according to the method used by the
> force field you are using.
> I would look at the section in the user guide dealing with this
> (
> http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields)
>
>
Is it true to optimize the molecule for example in gaussian(dft)first, and
then calculate the charges and make an .itp file for it?is it always
reliable?

> and then at the documentation for your force field!
>
> Cheers!
>
> On 13/04/18 11:21, leila karami wrote:
> > Dear gromacs users,
> >
> > I want to simulate a protein in different concentration of Fe3O4.
> >
> > How to obtain force field parameters of Fe3O4?
> >
> > Any help will highly be appreciated.
> >
> > Best,
>
>
> --
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[gmx-users] Polarizability analysis

[rose rahmani]

Hi

I did umbrella sampling and calculate PMF for different aminoacid in
different distance from surface. Now i want to discuss about the results.
First i used gmx sasa to prove that for example amino acid(tyrosine) with
more surface (it's aromatic) had more binding energy in comparison to
another...
But sometimes its hard to compare different AA, so i want to calculate AA's
polarizability. Is there any analysis in gromacs to calculate that?
If yes, is it probable that i get wrong results because some aminoacids are
not too different in size and polarizability? And are in SOL, so may affect
all these properties?
Do you have better idea?

Thank you so much
Rose
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[gmx-users] Gmx hbond

[rose rahmani]

Hi,

I have 2 questions, but please consider them 2 distinct questions and are
not related.
I did umbrella sapmling and calculate the PMF.
Now i I want to calculate number of hydrogen bonds for amino acid in its
initial distance(far from surface) and binding distance ( which is close to
surface and PMF is minimum there).
1- Is it rational to use pulling data(traj.xtc, .tpr,...) to calculate this
analysis, as it is nonequilibrium condition?
2- Is it better to choose initial frame and binding frame, do umbrella
sampling step (, nvt) and calculate number of hbons separately and compare
the result? Is it true to compare them in this condition?

With regards
Rose
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[gmx-users] Separate structure from box

[rose rahmani]

Hi,
I want to extract a structure in a box, i mean i want to extract a sheet
from the box of solution, because i dont have any separated .gro file from
my sheet. How can i do that?
Thank you
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Re: [gmx-users] Umbrella sampling

[rose rahmani]

Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?

On 3 Mar 2018 16:47, "Justin Lemkul" <jalem...@vt.edu> wrote:



On 3/3/18 7:02 AM, rose rahmani wrote:

> Hi
>
> I use umbrella sampling to calculate PMF, for studying the interaction of
> different aminoacids with nanosheet separately. But at the minimum distance
> from sheet, potential is zero for all PMF diagrams. I mean there isn't any
> positive potential even at closest distance of aminoacid from sheet. I did
> pulling and sampling manyyy times with different rates ...,still the same
> problem... how could it be possible?What is the problem? I really get
> confused. There isn't any closer distance to sample it.
> Would you please help me?
>

WHAM works by assigning the leftmost (lowest index) window a free energy
value of zero, and then constructs the rest of the profile relative to it.
You can adjust this with the -zprof0 option.

-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] Umbrella sampling

[rose rahmani]

Hi

I use umbrella sampling to calculate PMF, for studying the interaction of
different aminoacids with nanosheet separately. But at the minimum distance
from sheet, potential is zero for all PMF diagrams. I mean there isn't any
positive potential even at closest distance of aminoacid from sheet. I did
pulling and sampling manyyy times with different rates ...,still the same
problem... how could it be possible?What is the problem? I really get
confused. There isn't any closer distance to sample it.
Would you please help me?
With regards

-Rose
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[gmx-users] umbrella sampling

[rose rahmani]

 Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS
simulation for each window.

>> g_energy -f umbrella0.edr -o out.xvg
 1  Bond 2  Angle3  Proper-Dih.  4
Improper-Dih.
  5  LJ-146  Coulomb-14   7  LJ-(SR)  8
Coulomb-(SR)
  9  Coul.-recip.10  COM-Pull-En.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Conserved-En.   15  Temperature 16  Pressure

 17  Constr.-rmsd18  Vir-XX  19  Vir-XY  20  Vir-XZ

 21  Vir-YX  22  Vir-YY  23  Vir-YZ  24  Vir-ZX

 25  Vir-ZY  26  Vir-ZZ  27  Pres-XX 28  Pres-XY

 29  Pres-XZ 30  Pres-YX 31  Pres-YY 32  Pres-YZ

 33  Pres-ZX 34  Pres-ZY 35  Pres-ZZ 36
#Surf*SurfTen
 37  Mu-X38  Mu-Y

 39  Mu-Z40  Coul-SR:SOL-SOL

 41  LJ-SR:SOL-SOL   42  Coul-14:SOL-SOL

 43  LJ-14:SOL-SOL   44  Coul-SR:SOL-WAL

 45  LJ-SR:SOL-WAL   46  Coul-14:SOL-WAL

 47  LJ-14:SOL-WAL   48  Coul-SR:SOL-ZnS

 49  LJ-SR:SOL-ZnS   50  Coul-14:SOL-ZnS

 51  LJ-14:SOL-ZnS   52  Coul-SR:SOL-Protein

 53  LJ-SR:SOL-Protein   54  Coul-14:SOL-Protein

 55  LJ-14:SOL-Protein   56  Coul-SR:SOL-NA

 57  LJ-SR:SOL-NA58  Coul-14:SOL-NA  59  LJ-14:SOL-NA60
Coul-SR:SOL-CL
 61  LJ-SR:SOL-CL62  Coul-14:SOL-CL

 63  LJ-14:SOL-CL64  Coul-SR:SOL-wall0

 65  LJ-SR:SOL-wall0 66  Coul-14:SOL-wall0

 67  LJ-14:SOL-wall0 68  Coul-SR:SOL-wall1

 69  LJ-SR:SOL-wall1 70  Coul-14:SOL-wall1

 71  LJ-14:SOL-wall1 72  Coul-SR:WAL-WAL

 73  LJ-SR:WAL-WAL   74  Coul-14:WAL-WAL

 75  LJ-14:WAL-WAL   76  Coul-SR:WAL-ZnS

 77  LJ-SR:WAL-ZnS   78  Coul-14:WAL-ZnS

 79  LJ-14:WAL-ZnS   80  Coul-SR:WAL-Protein

 81  LJ-SR:WAL-Protein   82  Coul-14:WAL-Protein

 83  LJ-14:WAL-Protein   84  Coul-SR:WAL-NA

 85  LJ-SR:WAL-NA86  Coul-14:WAL-NA  87  LJ-14:WAL-NA88
Coul-SR:WAL-CL
 89  LJ-SR:WAL-CL90  Coul-14:WAL-CL

 91  LJ-14:WAL-CL92  Coul-SR:WAL-wall0

 93  LJ-SR:WAL-wall0 94  Coul-14:WAL-wall0

 95  LJ-14:WAL-wall0 96  Coul-SR:WAL-wall1

 97  LJ-SR:WAL-wall1 98  Coul-14:WAL-wall1

 99  LJ-14:WAL-wall1100  Coul-SR:ZnS-ZnS

101  LJ-SR:ZnS-ZnS  102  Coul-14:ZnS-ZnS

103  LJ-14:ZnS-ZnS  104  Coul-SR:ZnS-Protein

105  LJ-SR:ZnS-Protein  106  Coul-14:ZnS-Protein

107  LJ-14:ZnS-Protein  108  Coul-SR:ZnS-NA

109  LJ-SR:ZnS-NA   110  Coul-14:ZnS-NA 111  LJ-14:ZnS-NA   112
Coul-SR:ZnS-CL
113  LJ-SR:ZnS-CL   114  Coul-14:ZnS-CL

115  LJ-14:ZnS-CL   116  Coul-SR:ZnS-wall0

117  LJ-SR:ZnS-wall0118  Coul-14:ZnS-wall0

119  LJ-14:ZnS-wall0120  Coul-SR:ZnS-wall1

121  LJ-SR:ZnS-wall1122  Coul-14:ZnS-wall1

123  LJ-14:ZnS-wall1124  Coul-SR:Protein-Protein

125  LJ-SR:Protein-Protein  126  Coul-14:Protein-Protein

127  LJ-14:Protein-Protein  128  Coul-SR:Protein-NA

129  LJ-SR:Protein-NA   130  Coul-14:Protein-NA

131  LJ-14:Protein-NA   132  Coul-SR:Protein-CL

133  LJ-SR:Protein-CL   134  Coul-14:Protein-CL

135  LJ-14:Protein-CL   136  Coul-SR:Protein-wall0

137  LJ-SR:Protein-wall0138  Coul-14:Protein-wall0

139  LJ-14:Protein-wall0140  Coul-SR:Protein-wall1

141  LJ-SR:Protein-wall1142  Coul-14:Protein-wall1

143  LJ-14:Protein-wall1144  Coul-SR:NA-NA

145  LJ-SR:NA-NA146  Coul-14:NA-NA  147  LJ-14:NA-NA148
Coul-SR:NA-CL
149  LJ-SR:NA-CL150  Coul-14:NA-CL

151  LJ-14:NA-CL152  Coul-SR:NA-wall0

153  LJ-SR:NA-wall0 154  Coul-14:NA-wall0

155  LJ-14:NA-wall0 156  Coul-SR:NA-wall1

157  LJ-SR:NA-wall1 158  Coul-14:NA-wall1

159  LJ-14:NA-wall1 160  Coul-SR:CL-CL  161  LJ-SR:CL-CL162
Coul-14:CL-CL
163  LJ-14:CL-CL164  Coul-SR:CL-wall0

165  LJ-SR:CL-wall0 166  Coul-14:CL-wall0

167  LJ-14:CL-wall0 168  Coul-SR:CL-wall1

169  LJ-SR:CL-wall1 170  Coul-14:CL-wall1

171  LJ-14:CL-wall1 172  Coul-SR:wall0-wall0

173  LJ-SR:wall0-wall0  174  Coul-14:wall0-wall0

175  LJ-14:wall0-wall0  

[gmx-users] gmx distance

[rose rahmani]

Hi,
This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 400
nstxout  = 1000
nstvout  = 1000
nstfout  = 500
nstlog   = 500
nstenergy= 500
nstxtcout= 500
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = distance
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
---
pullx.xvg;

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.  4.287   1.76284
0.0500  4.287   1.75329
0.1000  4.287   1.74622
0.1500  4.287   1.73983
0.2000  4.287   1.73664
0.2500  4.287   1.7377
.
.

3999.7500   4.287   0.258632
3999.8000   4.287   0.258738
3999.8500   4.287   0.258955
3999.9000   4.287   0.260093
3999.9500   4.287   0.25843
4000.   4.287   0.258025
-
Then >>trjconv -f traj.xtc -s pull.tpr -n index.ndx -o confwhole.gro -pbc
whole
Then >>g_dist  -f confwhole.gro -n index.ndx -s pull.tpr -o distwhole.xvg

this is distwhole.xvg
   0.0001.76307740.0185155   -0.0197599   -1.7628694
   0.5001.7529889   -0.01330900.0135729   -1.7528858
   1.0001.7453604   -0.03446920.0751038   -1.7434030
   1.5001.7691813   -0.06215670.0087628   -1.7680674
.
.
3997.5001.61200060.9964043   -1.2400901   -0.2605782
3998.0001.61228910.9971979   -1.2404475   -0.2576084
3998.5001.61245740.9966092   -1.2406733   -0.2598433
3999.0001.61155650.9968075   -1.2396555   -0.2583475
3999.5001.61206160.9964568   -1.2404943   -0.2588253
4000.0001.61162940.9952377   -1.2410750   -0.2580390

as you see max dist=1.76 and min dist=1.611, but in VMD i can see that two
group (Protein and ZnS sheet) in last frame are too close to each other. so
why i see 1.611 in distwhole.xvg?

and could you please tell me what is the relevance of pullx.xvg to g_dist
output?as you see pullx.xvg ensure that distance between 2 group is
decreasing, so...?

is there anything i did not consider?

Thank you so much
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Re: [gmx-users] energy group exclusion

[rose rahmani]

Yes.
thank you so much

On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 1/14/18 9:59 AM, rose rahmani wrote:
>
>> Hello;
>>
>> this is md_pull.mdp
>>
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 100
>> nstxout  = 5000
>> nstvout  = 5000
>> nstfout  = 500
>> nstlog   = 500
>> nstenergy= 1000
>> nstxtcout= 1000
>> nstlist  = 10
>> rlist= 1.5
>> cutoff-scheme= Verlet
>> energygrp-excl   = WAL WAL ZnS ZnS
>> coulombtype  = pme
>> rcoulomb = 1.2
>> vdwtype  = Switch
>> rvdw_switch  = 1.0
>> rvdw = 1.2
>> pcoupl   = no
>> gen_vel  = no
>> constraints  = h-bonds
>> ns_type  = grid
>> pbc  = xy
>> freezegrps   = WAL ZnS
>> freezedim= Y Y Y Y Y Y
>> energygrps   = SOL WAL ZnS Protein NA CL
>> energygrp-excl   = WAL WAL ZnS ZnS
>> nwall= 2
>> wall-atomtype= C C
>> wall-type= 9-3
>> wall-density = 150 150
>> wall-ewald-zfac  = 3
>> ewald-geometry   = 3dc
>> fourierspacing   = 0.12
>> tcoupl   = v-rescale
>> tc-grps  = System
>> tau-t= 0.1
>> ref-t= 300
>>
>> ; Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= ZnS
>> pull_group2_name= Protein
>> pull_coord1_type= umbrella
>> pull_coord1_geometry= direction
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_vec = 0 0 1
>> pull_coord1_rate= -0.001
>> pull_coord1_k   = 5000
>> pull_coord1_start   = yes
>> pull_nstxout= 10
>>
>> --
>>
>> ERROR 1 [file md_pull.mdp]:
>>Energy group exclusions are not (yet) implemented for the Verlet scheme
>>
>>
>> WARNING 1 [file md_pull.mdp]:
>>Can not exclude the lattice Coulomb energy between energy groups
>>
>> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
>> Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
>> Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
>> Note that mdrun will redetermine rlist based on the actual pair-list setup
>> Calculating fourier grid dimensions for X Y Z
>> Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
>> Pull group  natoms  pbc atom  distance at start  reference at t=0
>> 1   560   280
>> 226   773   1.763 nm  1.763 nm
>> Estimate for the relative computational load of the PME mesh part: 0.77
>>
>> NOTE 3 [file md_pull.mdp]:
>>The optimal PME mesh load for parallel simulations is below 0.5
>>and for highly parallel simulations between 0.25 and 0.33,
>>for higher performance, increase the cut-off and the PME grid spacing.
>>
>>
>> This run will generate roughly 149 Mb of data
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> There were 3 notes
>>
>> There was 1 warning
>>
>> ---
>> Program gmx grompp, VERSION 5.1.4
>> Source code file:
>> /home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line:
>> 2107
>>
>> Fatal error:
>> There was 1 error in input file(s)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> i implemented  energygr-excl in mdp file, so why get this error?!
>>
>
> Read the above - such exclusions are not compatible with either the Verlet
> scheme or with PME.

Sorry, i couldn't understand "Read the above -such exclusions " ?

> and my second question is that i want to pull Protein(to get closer to
>> sheet) to ZnS sheet, so should i use position restraint for Protein in
>> this
>> step?
>>
&

[gmx-users] energy group exclusion

[rose rahmani]

Hello;

this is md_pull.mdp

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
cutoff-scheme= Verlet
energygrp-excl   = WAL WAL ZnS ZnS
coulombtype  = pme
rcoulomb = 1.2
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrps   = SOL WAL ZnS Protein NA CL
energygrp-excl   = WAL WAL ZnS ZnS
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= direction
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate= -0.001
pull_coord1_k   = 5000
pull_coord1_start   = yes
pull_nstxout= 10

--

ERROR 1 [file md_pull.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme


WARNING 1 [file md_pull.mdp]:
  Can not exclude the lattice Coulomb energy between energy groups

Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.208 nm, buffer size 0.008 nm
Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 36x36x300, spacing 0.111 0.111 0.120
Pull group  natoms  pbc atom  distance at start  reference at t=0
   1   560   280
   226   773   1.763 nm  1.763 nm
Estimate for the relative computational load of the PME mesh part: 0.77

NOTE 3 [file md_pull.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing.


This run will generate roughly 149 Mb of data

There were 3 notes

There was 1 warning

There were 3 notes

There was 1 warning

---
Program gmx grompp, VERSION 5.1.4
Source code file:
/home/sjalili/gromacs-5.1.4/src/gromacs/gmxpreprocess/grompp.c, line: 2107

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

i implemented  energygr-excl in mdp file, so why get this error?!

and my second question is that i want to pull Protein(to get closer to
sheet) to ZnS sheet, so should i use position restraint for Protein in this
step?
and what is the difference between geometry= direction or distance in my
system?

Would you please help me?

With regards
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Re: [gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

Oops,Sorrry. Sometimes big challenges make ones think hard and ignore
obvious issues.
Thank you so much Mr.justin and joao

On Sat, Jan 13, 2018 at 4:01 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> The output is very explicitly telling you what the problem is. You didn't
> provide a topology. Pass one the the -s flag.  How do you want the COM to
> be computed when you're not providing any masses?
>
> J
>
> On Jan 13, 2018 9:19 AM, "rose rahmani" <rose.rhm...@gmail.com> wrote:
>
> > I'm relly sorry for asking you again and again but...
> >
> > GROMACS:  gmx distance, VERSION 5.1.4
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >   gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
> > of group 6'
> >
> >
> > ---
> > Program: gmx distance, VERSION 5.1.4
> > Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
> > Function:void
> > gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::
> > SelectionCollection*)
> >
> > Inconsistency in user input:
> > No topology provided, but one is required for analysis
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------
> > Whai is the problem?;(
> >
> > On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 1/11/18 11:38 AM, rose rahmani wrote:
> > >
> > >>   [ ZnS ]
> > >> 123456789   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..
> > >>
> > >> [ Protein ]
> > >>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
> > >> 775
> > >>   776  777  778  779  780  781  782  783  784  785  786
> > >>
> > >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
> > >> "ZnS"
> > >> plus com of group "Protein"' -oxyz -oall
> > >> i exactly select index groups!!!
> > >> ---
> > >> Program: gmx distance, VERSION 5.1.4
> > >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> > >> Function:void gmx::SelectionCollection::setI
> > >> ndexGroups(gmx_ana_indexgrps_t*)
> > >>
> > >> Inconsistency in user input:
> > >> Invalid index group reference(s)
> > >>Cannot match 'group "ZnS"', because no such index group can be
> found.
> > >>Cannot match 'group "Protein"', because no such index group can be
> > >> found.
> > >>
> > >> For more information and tips for troubleshooting, please check the
> > >> GROMACS
> > >> website at http://www.gromacs.org/Documentation/Errors
> > >> 
> > >> -
> > >> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> > >> -select -oxyz
> > >> GROMACS:  gmx distance, VERSION 5.1.4
> > >> Executable:   /usr/local/gromacs/bin/gmx
> > >> Data prefix:  /usr/local/gromacs
> > >> Command line:
> > >>gmx distance -n index.ndx -f conf0.gro -select -oxyz
> > >>
> > >> Available static index groups:
> > >>   Group  0 "System" (4336 atoms)
> > >>   Group  1 "Other" (760 atoms)
> > >>   Group  2 "ZnS" (560 atoms)
> > >>   Group  3 "WAL" (200 atoms)
> > >>   Group  4 "NA" (5 atoms)
> > >>   Group  5 "CL" (5 atoms)
> > >>   Group  6 "Protein" (26 atoms)
> > >>   Group  7 "Protein-H" (12 atoms)
> > >> .
> > >> .
> > >> (one per line,  for status/groups, 'help' for help, Ctrl-D to
> > end)
> > >>
> > >>> 2
> > >>>
> > >> Selection '2' parsed
> > >>
> > >>> 6
> >

Re: [gmx-users] Umbrella sampling-gmx distance

[rose rahmani]

I'm relly sorry for asking you again and again but...

GROMACS:  gmx distance, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
of group 6'


---
Program: gmx distance, VERSION 5.1.4
Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300)
Function:void
gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::SelectionCollection*)

Inconsistency in user input:
No topology provided, but one is required for analysis

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Whai is the problem?;(

On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 1/11/18 11:38 AM, rose rahmani wrote:
>
>>   [ ZnS ]
>> 123456789   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..
>>
>> [ Protein ]
>>   761  762  763  764  765  766  767  768  769  770  771  772  773  774
>> 775
>>   776  777  778  779  780  781  782  783  784  785  786
>>
>> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group
>> "ZnS"
>> plus com of group "Protein"' -oxyz -oall
>> i exactly select index groups!!!
>> ---
>> Program: gmx distance, VERSION 5.1.4
>> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
>> Function:void gmx::SelectionCollection::setI
>> ndexGroups(gmx_ana_indexgrps_t*)
>>
>> Inconsistency in user input:
>> Invalid index group reference(s)
>>Cannot match 'group "ZnS"', because no such index group can be found.
>>Cannot match 'group "Protein"', because no such index group can be
>> found.
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> -
>> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
>> -select -oxyz
>> GROMACS:  gmx distance, VERSION 5.1.4
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>gmx distance -n index.ndx -f conf0.gro -select -oxyz
>>
>> Available static index groups:
>>   Group  0 "System" (4336 atoms)
>>   Group  1 "Other" (760 atoms)
>>   Group  2 "ZnS" (560 atoms)
>>   Group  3 "WAL" (200 atoms)
>>   Group  4 "NA" (5 atoms)
>>   Group  5 "CL" (5 atoms)
>>   Group  6 "Protein" (26 atoms)
>>   Group  7 "Protein-H" (12 atoms)
>> .
>> .
>> (one per line,  for status/groups, 'help' for help, Ctrl-D to end)
>>
>>> 2
>>>
>> Selection '2' parsed
>>
>>> 6
>>>
>> Selection '6' parsed
>>
>
> You should be selecting 'com of group 2' etc. here to get what you want. I
> don't know why the command-line version of this didn't work, but to get a
> COM distance, you need to tell gmx distance to do it, otherwise it's just
> going to produce pairwise distances, which is what you're asking for here.
>
> -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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

[rose rahmani]

I had this problem but i couldn't solve it.
 But i can tell you just a temporary solution; Don't use -sep with
trjconv,then use the output conf as an input for gmx distance. it probably
gives you sth like this;

time   distances
   0.0001.75372870.02386010.0428935   -1.7530417
   2.0001.7294775   -0.0426260   -0.0664551   -1.7276745
   4.0001.71536770.06641650.0698769   -1.7126565
  .
.
.
.
just consider that time=2 >>> is 1 ps ( depends on dt )
  =4  >>> is  2ps
  = 6  >>> is  3ps .
but distances are exactly the same.
Sorrry, i know maybe Dr.justin and all professionals don't agree with these
solutions, but i can understand,when you don't get a proper answer,
sometimes you have to ridiculous solutions.That's it!


On Fri, Jan 12, 2018 at 10:44 AM, "Ashwini Londhe" <615...@kist.re.kr>
wrote:

>
>
>
> Hi
>
>
> Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very
> fine. so I following the same tutorial for ligand-protein complex.
>
>
> I have pulled the ligand over 300ps using following MD_pull.mdp and also
> generated  series of cordinate files (conf0.gro-conf300.gro) but problem is
> at distance calculation.
>
>
>
>
>
> title = Umbrella pulling simulation
>
>
> define = -DPOSRES
>
> ; Run parameters
>
> integrator = md
>
> dt = 0.002
>
> tinit = 0
>
> nsteps = 15 ; 300 ps
>
>
> nstcomm = 10
>
> ; Output parameters
>
> nstxout = 5000 ; every 10 ps
>
> nstvout = 5000
>
> nstfout = 500
>
> nstxtcout = 500 ; every 1 ps
>
> nstenergy = 500
>
> ; Bond parameters
>
> constraint_algorithm = lincs
>
>
> constraints = all-bonds
>
> continuation = yes ; continuing from NPT
>
> ; Single-range cutoff scheme
>
> nstlist = 5
>
> ns_type = grid
>
> rlist = 1.4
>
> rcoulomb = 1.4
>
> rvdw = 1.4
>
> ; PME electrostatics parameters
>
> coulombtype = PME
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> pme_order = 4
>
> ewald_rtol = 1e-5
>
> optimize_fft = yes
>
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = Nose-Hoover
>
> tc_grps = Protein Non-Protein
>
> tau_t = 0.5 0.5
>
> ref_t = 310 310
>
> ; Pressure coupling is on
>
> Pcoupl = Parrinello-Rahman
>
> pcoupltype = isotropic
>
> tau_p = 1.0
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> refcoord_scaling = com
>
> ; Generate velocities is off
>
> gen_vel = no
>
> ; Periodic boundary conditions are on in all directions
>
> pbc = xyz
>
> ; Long-range dispersion correction
>
> DispCorr = EnerPres
>
> ; Pull code
>
> pull = yes
>
> pull_ngroups = 2
>
> pull_ncoords = 1
>
>
> pull_group1_name = Protein
>
>
> pull_group2_name = L6I
>
>
> 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 ns
>
>
> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
>
>
> pull_coord1_start = yes ; define initial COM distance > 0
>
>
>
>
>
> I have used distances.pl file from gromacs tutorial and change the group
> name Chain_A and Chain_B with L6I and Protein. Also replaced 500 frames
> with 300 frames. It generated summary_distance.dat file which does not
> include distances values.
>
>
>  After running script it generates this at the end
>
>
> .
>
>
> .
>
>
> .
>
>
> Processing configuration 300...
>
>
> readline () on closed filehandle IN at distances.pl line 16.
>
>
> Use of uninitializd value $distance in concatenaton (.) or string at
> distans.pl line 30
>
>
>
>
>
> How could it happen by just changing Chain_A to L6I and Chain_B to Protein
> and conformations 500 to 300 it seems script works fine for peptide system
> only and not for protein_ligand complex.
>
>
>
>
>
> Also above error generated for ony proein-ligand complex and not for the
> peptide tutoral.
>
>
> Please help me to sort out this problem.
>
>
>
>
>
> Regards
>
>
> Ashwini Londhe
>
>
>
> Korea Institute of Science and Technology (KIST)
> 5, Hwarang-ro 14-gil
> Seongbuk-gu
> Seoul, 02792
> Republic of Korea
>
>
> (우: 02792) 서울특별시 성북구 화랑로 14길 5
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[gmx-users] gmx distance

[rose rahmani]

Hi

i'm doing umbella sampling. whenever i use gmx distance after pulling in
V.5.1.4 , i wouldn't have proper dist.xvg file.
I did what you said Mr.Justin ( as you refered me to this link
http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-dist)
but still there are some problems.

[ ZnS ]
   123456789   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..

[ Protein ]
 761  762  763  764  765  766  767  768  769  770  771  772  773  774  775
 776  777  778  779  780  781  782  783  784  785  786

command; gmx distance -n index.ndx -f conf0.gro -select 'com of group "ZnS"
plus com of group "Protein"' -oxyz -oall
i exactly select index groups!!!
---
Program: gmx distance, VERSION 5.1.4
Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
Function:void gmx::SelectionCollection::setI
ndexGroups(gmx_ana_indexgrps_t*)

Inconsistency in user input:
Invalid index group reference(s)
  Cannot match 'group "ZnS"', because no such index group can be found.
  Cannot match 'group "Protein"', because no such index group can be found.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-
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