[gmx-users] Gromacs installation to do coupled QMMM with Gaussian

[Maryam Kowsar]

Dear all,

How can I compile Gromacs for doing QMM/MM computations with Gaussian ? Is
there a special flag during installation process? I have read the
instructions in
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
But it is not a step by step instruction. Your help would be appreciated.

Thank you.
Best
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[gmx-users] MSD

[Maryam Kowsar]

Dear all

I want to calculate the MSD of a group of molecules in my system. In the
.mdp file, xtc_grps is set for this group only. When I use g_msd - n  -f
 -o (-mol does not work) and select the mentioned group, it stops after a
while in the 2000th frame. Is there anything wrong with the simulation,
.mdp or command?
Thanks.
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Re: [gmx-users] Force field for ion-carbon interaction

[Maryam Kowsar]

Thank you very much Alex :)

On Thursday, December 22, 2016, Alex <nedoma...@gmail.com> wrote:

> Sorry to hear this. There is a good chance your reviewer is being an
> obtuse donkey. As a fellow modeler and also a referee, I'd be much more
> worried if someone _did not_ use a standard and well-tested description for
> ions.
>
> Best of luck! :)
>
> Alex
>
>
> On 12/21/2016 11:40 PM, Maryam Kowsar wrote:
>
>> Thank you Alex. Actually I used Amber since I havent found any better
>> force
>> fields for nonbonded interactions in my system. It worked fine, but that
>> was questioned by a reviewer of my submitted paper, though I provided
>> references.
>>
>> On Wednesday, December 21, 2016, Alex <nedoma...@gmail.com> wrote:
>>
>> Hi Maryam,
>>>
>>> I am not really sure what "most proper" means when it comes to MD
>>> simulations, but I think if we're talking about vdw/electrostatics, AMBER
>>> and OPLS-AA are very close and have been used widely in the presence of
>>> things like CNTs and graphene... If there's any particular effect you are
>>> unable to reproduce with those ion descriptions, that is of course a
>>> different problem.
>>>
>>> Hope this helps.
>>>
>>> Alex
>>>
>>> On Wed, Dec 21, 2016 at 12:10 PM, Maryam Kowsar <maryam.kow...@gmail.com
>>> >
>>> wrote:
>>>
>>> Dear all
>>>>
>>>> What is the best and most proper force field for ions (like Na+ and
>>>> Ca2+)
>>>> and carbon structured systems interactions? I found a few papers which
>>>>
>>> used
>>>
>>>> Amber force field. Has anyone worked with or seen any papers in this
>>>> regard?
>>>> Thanks.
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[gmx-users] Force field for ion-carbon interaction

[Maryam Kowsar]

Dear all

What is the best and most proper force field for ions (like Na+ and Ca2+)
and carbon structured systems interactions? I found a few papers which used
Amber force field. Has anyone worked with or seen any papers in this
regard?
Thanks.
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[gmx-users] all electron force field

[Maryam Kowsar]

Dear all,

I need to use a potential in which electrons are also considered for my
simulations in Gromacs. I found the all-electron force field which is
already implemented in Lammps package. Is it possible to use or implement
it in GROMACS? Can i use QM/MM calculations in Gromacs instead? Also, it is
suggested to use the polarizable force field like OPLS-AAP. Does it have
the same functions as all electron force field?

Thank you.
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[gmx-users] electrostatic energy calculation

[Maryam Kowsar]

Thank you all. What James suggested seems to work. I just wonder what the
benefit of rerun option is. If I start the run from the begining with a
change in .mdp it leads to the same results I suppose.
Thanks.

On Tuesday, August 2, 2016, Mark Abraham <mark.j.abra...@gmail.com
<javascript:_e(%7B%7D,'cvml','mark.j.abra...@gmail.com');>> wrote:

> Yes, as I said.
>
> Mark
>
> On Tue, 2 Aug 2016 15:31 <jkrie...@mrc-lmb.cam.ac.uk> wrote:
>
> > Thanks Justin and Mark. Yes that could be it. I thought I had tried both
> > two and more energygrps with and without GPU and that two had worked on
> > both but I can only find logs with more than two energygrps for the jobs
> > with GPU. I can't see any kind of warning. I am using GROMACS 5.0.4 - do
> > you mean a newer version than that would bring this up better?
> >
> > Best wishes
> > James
> >
> > > Hi,
> > >
> > > Rerun works with any number of energy groups, but probably what you've
> > > done
> > > is run one of your reruns on a GPU, which doesn't support energy
> groups,
> > > and missed the warning mdrun issues. Recent versions are more helpful
> at
> > > bringing this to your attention.
> > >
> > > Mark
> > >
> > > On Tue, Aug 2, 2016 at 1:54 PM <jkrie...@mrc-lmb.cam.ac.uk> wrote:
> > >
> > >> That's interesting Alex. mdrun -rerun only works with two energygrps
> (I
> > >> put more then all g_energy terms come to zero) but you're saying
> normal
> > >> mdrun works with any number. I don't know if that's intentional or
> > >> whether
> > >> the developers would like me to make a Redmine..
> > >>
> > >> > Hi there,
> > >> >
> > >> > g_energy or gmx energy just lists the short-ranged non-bonded
> > >> potential
> > >> > energies of those species which have been already indicated in *.mdp
> > >> file
> > >> > by "energygrps", like energygrps   = A B C, then g_energy would
> offer
> > >> you
> > >> > something like  Coul-SR: A-B , LJ-SR: B-C and so on.
> > >> >
> > >> > Cheers,
> > >> > Alex
> > >> >
> > >> > On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar
> > >> <maryam.kow...@gmail.com>
> > >> > wrote:
> > >> >
> > >> >> Dear all,
> > >> >>
> > >> >> I want to calculate the electrostatic energy (coulomb SR and LR)
> for
> > >> a
> > >> >> set
> > >> >> of molecules during the whole simulation. I used g_energy -f
> ener.edr
> > >> -o
> > >> >> (with or without -nmol option), but it only gives me 1 average
> output
> > >> >> for
> > >> >> the last step.I tried g_enemat -f -etot (-emat) but it stops
> needing
> > >> a
> > >> >> group.dat file. Is there a way to calculate coulomb energy in all
> > >> steps
> > >> >> preferably for a set of desired charged molecules?
> > >> >> Thanks.
> > >> >> --
> > >> >> Gromacs Users mailing list
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> > >> >> posting!
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> > >> >>
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> > >> Gromacs Users maili

[gmx-users] electrostatic energy calculation

[Maryam Kowsar]

Dear all,

I want to calculate the electrostatic energy (coulomb SR and LR) for a set
of molecules during the whole simulation. I used g_energy -f ener.edr -o
(with or without -nmol option), but it only gives me 1 average output for
the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
group.dat file. Is there a way to calculate coulomb energy in all steps
preferably for a set of desired charged molecules?
Thanks.
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Re: [gmx-users] Extending simulations

[Maryam Kowsar]

Hi

I think it should be like this:
tpbconv -s previous.tpr -extend timetoextendby -o new.tpr
mdrun -s new.tpr -cpi previous.cpt


On Tue, Dec 22, 2015 at 2:07 PM, Mark Abraham 
wrote:

> Hi,
>
> Please start with
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> Mark
>
> On Tue, Dec 22, 2015 at 9:10 PM masoud keramati  >
> wrote:
>
> > sorry with my question
> >
> > is it true that for extending simulation use the following code?
> >
> > gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr
> > gmx mdrun -deffnm md2
> >
> > *md.gro and md.trr is files for first run
> >
> > On 12/22/15, Justin Lemkul  wrote:
> > >
> > >
> > > On 12/21/15 7:00 PM, Soumya Lipsa Rath wrote:
> > >> Dear Mark and Chandan,
> > >>
> > >> Thank you so much for the information. I was indeed using a wrong tpr
> > >> file.
> > >> I will include the -cpi state.cpt flag during the tpbconv step.
> > >>
> > >
> > > You don't need -cpi with tpbconv, only in mdrun.
> > >
> > > -Justin
> > >
> > >> Thanks,
> > >>
> > >> Soumya
> > >>
> > >> On Mon, Dec 21, 2015 at 12:30 PM, Soumya Lipsa Rath
> > >>  > >>> wrote:
> > >>
> > >>> Dear Gromacs users,
> > >>>
> > >>> I am trying to extend my simulation for 200ns by using:
> > >>>
> > >>> tpbconv_mpi -s topol.tpr -extend 20 -o topol2.tpr
> > >>> mdrun_mpi -s topol2.tpr -cpi state.cpt -append -maxwarn 5 >&
> > >>> grompp_output.log
> > >>>
> > >>> However, my simulation has only extended for 50ns. Am I doing
> something
> > >>> wrong?
> > >>>
> > >>> Thanks,
> > >>>
> > >>> Soumya
> > >>>
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
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Re: [gmx-users] electric field

[Maryam Kowsar]

Thank you Erik and Viet Man!

On Mon, Nov 16, 2015 at 6:24 PM, Man Hoang Viet <mhv...@ifpan.edu.pl> wrote:

> Hi,
>
> I can confirm electric field (even laser-pulse form) in GROMACS (all
> version from 3.0 to current newest one) work fine. To check it, you may
> consider a system containing only an ion (say Na+) in vacuum and set mdp
> file as:
> ###
> dt  =  0.0002; ps !
> nsteps  =  100  ; total 20 fs
>
> ...
>
> Tcoupl  =  no
> Pcoupl  =  no
> gen_vel =  no
> E-x =  1 30 1
> 
>
> After run MD you may check the velocity of the ion and see how it work by
> some general motion equations such as Force = -q*E = m*a -->
> veleocity=a*t.
>
> Additionally, the option -field of mdrun will give output of electric
> field.
>
> Good luck!
>
> Viet Man
>
>
> > Date: Sun, 15 Nov 2015 22:58:34 +0330
> > From: Maryam Kowsar <maryam.kow...@gmail.com>
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] electric field
> > Message-ID:
> >   <CAK1iX1UrqgQ61-VCbEg8-dMLjQXs+6KuERQ7m47SzxFy4ubk=
> a...@mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Dear users,
> >
> > I applied electric fields of different magnitudes (less than 1 v/nm since
> > higher amounts are avoided) in my system. I have some charged water
> > molecules and I expected to see very different results when the magnitude
> > is changed, but haven't got that much difference. How can I be sure that
> > electric fields worked?
> > I found the following link that it changed the code of electric field
> > according to the shape of the system:
> >  http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun
> > Can the current implemented code in gromacs be applied for all systems or
> > should I change it for different systems?
> >
> > Thanks!
>
>
>
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[gmx-users] electric field

[Maryam Kowsar]

Dear users,

I applied electric fields of different magnitudes (less than 1 v/nm since
higher amounts are avoided) in my system. I have some charged water
molecules and I expected to see very different results when the magnitude
is changed, but haven't got that much difference. How can I be sure that
electric fields worked?
I found the following link that it changed the code of electric field
according to the shape of the system:
 http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun
Can the current implemented code in gromacs be applied for all systems or
should I change it for different systems?

Thanks!
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[gmx-users] output control

[Maryam Kowsar]

Dear users,

I have a simulation which lasts in 2ns and has around 4G trajectory if Iset
nstxout = 1000. I need the output file of coordinates and velocities
written every step which means a 4000G output file! Is there a way that I
can manage the tarjectory so that only in the last 200ps of simulation it
is written every step? If not, can I set nstxout = 1000 and get data for
every step after the simulation?

Thank you.
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Re: [gmx-users] output control

[Maryam Kowsar]

Thanks Pierre.
What if I dont want to stop the simulation and use its output as the input
for the next simulation?

On Mon, Oct 12, 2015 at 10:15 AM, Pierre Ghesquiere <
pierre.ghesqui...@univ-perp.fr> wrote:

> Hi,
>
> I think you could do two successive trajectories. One during the 1.8 ns
> and another of 200ps. Then you use different writing frequencies for the
> two simulations.
>
> --
> P.
>
> Maryam Kowsar <maryam.kow...@gmail.com> a écrit :
>
> Dear users,
>>
>> I have a simulation which lasts in 2ns and has around 4G trajectory if
>> Iset
>> nstxout = 1000. I need the output file of coordinates and velocities
>> written every step which means a 4000G output file! Is there a way that I
>> can manage the tarjectory so that only in the last 200ps of simulation it
>> is written every step? If not, can I set nstxout = 1000 and get data for
>> every step after the simulation?
>>
>> Thank you.
>> --
>> Gromacs Users mailing list
>>
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>> posting!
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>>
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Re: [gmx-users] output control

[Maryam Kowsar]

Thanks Mark and Pierre.

I would rather try Mark's solution but I exactly dont understand what I
should do now! I used 2 sets of commands

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr

mdrun -s next.tpr -cpi previous.cpt

OR

 tpbcov -s -o new.tpr -extend 20

grompp -f new.mdp(NSTXOUT=1) -c old.tpr -o new.tpr

mdrun -s new.tpr -cpi

which will generate 200G data!

your help is needed!

Thanks.


​
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Re: [gmx-users] output control

[Maryam Kowsar]

Yes of course! That would be so kind of you to send the editor and a brief
description of how it works.
Thanks a lot tsjerk.

On Monday, October 12, 2015, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi Maryam,
>
> You only need a modified TPR file. There's no need to hassle with
> structures, as that's all in the checkpoint file.
>
> I have a TPR editor that allows changing things like nstxout. So you can
> run the first part of the simulation, then modify the TPR nstxout and
> nsteps, and continue the simulation from the last checkpoint file. If you
> want, I can send that.
>
> Cheers,
>
> Tsjerk
> On Oct 12, 2015 5:35 PM, "Maryam Kowsar" <maryam.kow...@gmail.com
> <javascript:;>> wrote:
>
> > Thanks Mark and Pierre.
> >
> > I would rather try Mark's solution but I exactly dont understand what I
> > should do now! I used 2 sets of commands
> >
> > tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> >
> > mdrun -s next.tpr -cpi previous.cpt
> >
> > OR
> >
> >  tpbcov -s -o new.tpr -extend 20
> >
> > grompp -f new.mdp(NSTXOUT=1) -c old.tpr -o new.tpr
> >
> > mdrun -s new.tpr -cpi
> >
> > which will generate 200G data!
> >
> > your help is needed!
> >
> > Thanks.
> >
> >
> > ​
> > --
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> >
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[gmx-users] New atom definition

[Maryam Kowsar]

Dear all,

I want to use some atoms that are not implemented in gromacs. If i even
make a .gro file, making a topology is a problem. What should i do?

Thanks!
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Re: [gmx-users] New atom definition

[Maryam Kowsar]

Thaks justin!
I did it several times and it worked. But now when i want to add some
neutral gas or heavy atoms it stops me with the error that the atom is not
defined. I dont know where i make a mistake.

On Friday, September 18, 2015, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/17/15 3:08 PM, Maryam Kowsar wrote:
>
>> Dear all,
>>
>> I want to use some atoms that are not implemented in gromacs. If i even
>> make a .gro file, making a topology is a problem. What should i do?
>>
>>
> Derive parameters in a manner consistent with the desired force field and
> add all necessary bonded and nonbonded parameters to ffbonded.itp and
> ffnonbonded.itp.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Maryam Kowsar]

Hi dan
I think that's not possible to change forcefield parameters and use the old
defined forcefield like opls. When you change the parameters in .itp you
should introduce your own forcefield. Try to have all the needed files of
forcefield in a new folder and use that during making topology.

On Tuesday, September 8, 2015, Phwey Gil  wrote:

> Hi,
>
> I am looking to specify my own parameters for LJ parameters. Using the OPLS
> forcefield, I only want to change the LJ parameters of some atoms.
>
> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
> change the LJ parameters for the hydrogens in C8H16O2 only.
>
> I have tried specifying [ atomtypes ] in various places (In .top or .itp)
> using the following format:
>
>  [ atomtypes ]
>   H H  1.008  0.450 A   5.66387665E-4
> 2.80730518E-7
>
> But I was not successful; I checked topol.tpr and the numbers are according
> to OPLS and not my specified values.
>
> Can someone give me advice on how to do this? I've checked the forums and I
> was not successful at finding the correct information.
>
> Best Regards,
>
> Dan
>
> --
> Dan Gil
> Case Western Reserve University | Class of 2016
> Researcher, Department of Chemical Engineering
> ps...@case.edu 
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Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Maryam Kowsar]

Hi justin
Actually i modified the forcefield parameters to introduce atoms that are
not present in that. I think you are right in the case that we want to
change bonded or nonbonded parameters in the forcefield

On Wednesday, September 9, 2015, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/9/15 7:29 AM, Maryam Kowsar wrote:
>
>> Hi dan
>> I think that's not possible to change forcefield parameters and use the
>> old
>> defined forcefield like opls. When you change the parameters in .itp you
>> should introduce your own forcefield. Try to have all the needed files of
>> forcefield in a new folder and use that during making topology.
>>
>>
> This is not true. Any force field can be modified or extended. A local
> copy of a modified force field is a safe recommendation, but in the case of
> simply adding new atom types, there's little harm that can be done.
>
> -Justin
>
> On Tuesday, September 8, 2015, Phwey Gil <ps...@case.edu> wrote:
>>
>> Hi,
>>>
>>> I am looking to specify my own parameters for LJ parameters. Using the
>>> OPLS
>>> forcefield, I only want to change the LJ parameters of some atoms.
>>>
>>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
>>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
>>> change the LJ parameters for the hydrogens in C8H16O2 only.
>>>
>>> I have tried specifying [ atomtypes ] in various places (In .top or .itp)
>>> using the following format:
>>>
>>>   [ atomtypes ]
>>>H H  1.008  0.450 A   5.66387665E-4
>>> 2.80730518E-7
>>>
>>> But I was not successful; I checked topol.tpr and the numbers are
>>> according
>>> to OPLS and not my specified values.
>>>
>>> Can someone give me advice on how to do this? I've checked the forums
>>> and I
>>> was not successful at finding the correct information.
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
>>> --
>>> Dan Gil
>>> Case Western Reserve University | Class of 2016
>>> Researcher, Department of Chemical Engineering
>>> ps...@case.edu <javascript:;>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
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>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org <javascript:;>.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] topology parameters

[Maryam Kowsar]

Thanks Vitaly!

On Sun, Sep 6, 2015 at 3:29 PM, Vitaly V. Chaban  wrote:

> Bonded interactions are important. Sections are for human understanding.
>
>
>
>
> On Sun, Sep 6, 2015 at 3:36 AM, mah maz  wrote:
> > Dear users,
> >
> > Are resnr, residue, moleculetype, system and molecules names in .top file
> > important? I have a CNT containing water molecules. I can see weather I
> > assign CNT to all the molecules as residue names Or CNT and water,
> results
> > are the same. Also if I use 1 for CNT as resdnr and 2 for water Or 1 for
> > all of them I get the same results! Are they only names or something else
> > eg. type is important in this case?
> >
> > Thanks!
> > --
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> posting!
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[gmx-users] charge in *.n2t file

[Maryam Kowsar]

Hi Hassan,

Charges depends on your system. You can find it either from the related
articles or calculate it yourself.

On Thu, Aug 13, 2015 at 11:08 AM, حسن هاشم زاده hashemzadehas...@gmail.com
javascript:_e(%7B%7D,'cvml','hashemzadehas...@gmail.com'); wrote:

 hi all
 I use from charmm27.ff force field for my work. below listed the
 parameter which i used in *.n2t file.  how can find or calculate  charge
 for each atoms (the third column) for charmm27 force field


 CCA???   12.011  2C 0.142   C 0.142
 CCA0.00   12.011  3C 0.142   C 0.142   C 0.142
 CCA0.00   12.011  3C 0.142   C 0.142   H 0.108
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Re: [gmx-users] bonded parameter

[Maryam Kowsar]

Hi Hassan,
For making a topology(.top) file all parameters of your forcefield is
needed.

On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده hashemzadehas...@gmail.com
wrote:

 Hi

 ?Which step of simulation the bonded parameters of available in a force
 field will be used
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Re: [gmx-users] force field

[Maryam Kowsar]

let me modify my previous message: in the g_x2top command, not grompp :-)

On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com
wrote:

 Hi Mohammad,

 Yes that's possible. You should just have the necessary files of your
 desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
 command just add -ff folder name. that's all! It will use your forcefield
 instead of the present forcefields in gromacs.

 Regards,
 -Maryam

 On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com
 wrote:

 Hi;
 I want to use ff14SB Amberprotein force field. But it isn't included in
 the gromacs force fields list.Is it possible to use this force field? How
 can I add it in?Thank you, Mohammad.
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Re: [gmx-users] force field

[Maryam Kowsar]

I did a similar task. You should know the parameters and convert your files
format to gromacs format. A bit difficult but possible.


On Sun, Aug 9, 2015 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 8/9/15 12:59 PM, mohammad r wrote:

 Thank you MaryamI want to use this force field in the first step of
 generating the topology file (pdb2gmx command in the force field shown
 after this command). Is it possible? and unfortunately I don't know how to
 find the necessary files of this force field. I searched a lot but I didn't
 succeed.


 If the force field files haven't been created already (in this case, they
 haven't) you have to convert the force field files from AMBER format to
 GROMACS format.  That's a pretty big undertaking if you're not well versed
 in the formats.

 I have another question, is it possible to acetylate or ammoniate a
 peptide with gromacs?


 Anything is possible, provided you have parameters for such species.

 -Justin

 thank you, M.


   On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar 
 maryam.kow...@gmail.com wrote:


   let me modify my previous message: in the g_x2top command, not grompp
 :-)
 On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com
 wrote:

 Hi Mohammad,
 Yes that's possible. You should just have the necessary files of your
 desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
 command just add -ff folder name. that's all! It will use your forcefield
 instead of the present forcefields in gromacs.
 Regards,-Maryam
 On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com
 wrote:

 Hi;
 I want to use ff14SB Amberprotein force field. But it isn't included in
 the gromacs force fields list.Is it possible to use this force field? How
 can I add it in?Thank you, Mohammad.
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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

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Re: [gmx-users] force field

[Maryam Kowsar]

Hi Mohammad,

Yes that's possible. You should just have the necessary files of your
desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
command just add -ff folder name. that's all! It will use your forcefield
instead of the present forcefields in gromacs.

Regards,
-Maryam

On Sun, Aug 9, 2015 at 5:57 PM, mohammad r mohammad.r0...@yahoo.com wrote:

 Hi;
 I want to use ff14SB Amberprotein force field. But it isn't included in
 the gromacs force fields list.Is it possible to use this force field? How
 can I add it in?Thank you, Mohammad.
 --
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Re: [gmx-users] magnetic field - segmentation fault

[Maryam Kowsar]

Thank you Erik!

On Sun, Jul 26, 2015 at 2:49 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:

 Dear Maryam,

 I usually like to keep it simple and use gdb. That said, clang+lldb is a
 great compiler+debugger combo. Valgrind may also be helpful.

 Kind regards,
 Erik

  On 24 Jul 2015, at 18:02, Maryam Kowsar maryam.kow...@gmail.com wrote:
 
  Dear Erik,
 
  Thank you! My sleeves are rolled up for several days! Which debugger do
 you
  suggest?
 
  Dear Man Hong,
 
  It seems we are looking at the problem from 2 different angles. Well, I
 am
  going to test it, but I think it's not logical; without T-coupling we
 can't
  rely on the results. However, I wonder why you think it may cause
 problems.
  Velocities should change. I guess I can ask you questions then. Which
  version of gromacs are you working with? Which source codes have you
  modified?
  Thank you!
 
  On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet mhv...@ifpan.edu.pl
 wrote:
 
  Hi Maryam Kowsar,
 
  I have implemented external magnetic field to GROMACS and tested it. The
  code ran well and the test result is consistent with experiment for
 simple
  case (say Na+ in vacuum and without t_coupling). I may guest why your
 code
  got the error. But I am sorry that I can not share my code to anyone now
  (but I will do share it to this forum in near future).
  However, there is an important issue that MD simulation with t_coupling
  always does re-scale velocity of all atoms to keep the given temperature
  and it strongly effect on the Lorentz Force of the external magnetic
  field. Otherwise, If the t_coupling is not applied, the system
 temperature
  will increase forever. Therefore, I wonder whether we really can
 estimate
  effect of the magnetic field on protein (or other target) in simulation?
 
 
  On 23 Jul 2015, at 11:52, Maryam Kowsar maryam.kow...@gmail.com
 wrote:
 
  Dear users,
 
  Iam trying to add magnetic field code to gromacs. I think I did all the
  modifications necessary in all source codes but when I use mdrun
 command
  it
  gives me segmentation fault error while in md.log the magnetic field
 is
  present. When I change tpx_version the error is gone but in md.log no
  magnetic field is implemented. How can I overcome segmentation fault
  error?  Should tpx_version be changed after adding a code?
 
  Thanks!
 
  Man Hoang Viet
  Institute of Physics,
  Polish Academy of Sciences.
  Al. Lotnikow 32/46
  02-668 Warsaw, Poland.
 
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Re: [gmx-users] magnetic field - segmentation fault

[Maryam Kowsar]

Dear Erik,

Thank you! My sleeves are rolled up for several days! Which debugger do you
suggest?

Dear Man Hong,

It seems we are looking at the problem from 2 different angles. Well, I am
going to test it, but I think it's not logical; without T-coupling we can't
rely on the results. However, I wonder why you think it may cause problems.
Velocities should change. I guess I can ask you questions then. Which
version of gromacs are you working with? Which source codes have you
modified?
Thank you!

On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet mhv...@ifpan.edu.pl wrote:

 Hi Maryam Kowsar,

 I have implemented external magnetic field to GROMACS and tested it. The
 code ran well and the test result is consistent with experiment for simple
 case (say Na+ in vacuum and without t_coupling). I may guest why your code
 got the error. But I am sorry that I can not share my code to anyone now
 (but I will do share it to this forum in near future).
 However, there is an important issue that MD simulation with t_coupling
 always does re-scale velocity of all atoms to keep the given temperature
 and it strongly effect on the Lorentz Force of the external magnetic
 field. Otherwise, If the t_coupling is not applied, the system temperature
 will increase forever. Therefore, I wonder whether we really can estimate
 effect of the magnetic field on protein (or other target) in simulation?


 On 23 Jul 2015, at 11:52, Maryam Kowsar maryam.kow...@gmail.com wrote:

  Dear users,
 
  Iam trying to add magnetic field code to gromacs. I think I did all the
  modifications necessary in all source codes but when I use mdrun command
  it
  gives me segmentation fault error while in md.log the magnetic field is
  present. When I change tpx_version the error is gone but in md.log no
  magnetic field is implemented. How can I overcome segmentation fault
  error?  Should tpx_version be changed after adding a code?
 
  Thanks!

 Man Hoang Viet
 Institute of Physics,
 Polish Academy of Sciences.
 Al. Lotnikow 32/46
 02-668 Warsaw, Poland.

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[gmx-users] magnetic field - segmentation fault

[Maryam Kowsar]

Dear users,

Iam trying to add magnetic field code to gromacs. I think I did all the
modifications necessary in all source codes but when I use mdrun command it
gives me segmentation fault error while in md.log the magnetic field is
present. When I change tpx_version the error is gone but in md.log no
magnetic field is implemented. How can I overcome segmentation fault
error?  Should tpx_version be changed after adding a code?

Thanks!
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Re: [gmx-users] freezing graphene sheet

[Maryam Kowsar]

That's probably because of your forcefield. But if you want to freeze atoms
or groups, you can simply do it by freeezgrps and freezedim in your
.mdp file. In the former you should assign the groups you want to freeze
and in the latter the directions, eg. 'Y,Y,Y' which means freezing in x,y
and z directions.

On Sat, Jul 4, 2015 at 1:49 PM, Alex nedoma...@gmail.com wrote:

 I assume by deformed you mean non-flat. Finite graphene flakes in
 vacuum will not stay flat, that's their physics. They also won't be
 exactly flat in a periodic system, or even if you restrain the edge
 atoms, graphene will still be rippled at any nonzero temperature away
 from the edges.

 So, why exactly do you want to freeze anything?

 Alex


 GR Dear all,
 GR I have simuated graphene and surfactants for 10 ns. When I visualized
 it by
 GR VMD, I saw that my graphene sheet was deformed. I put graphene finite.
 I am
 GR trying  to freeze graphene sheet but I am not sure about the my mdp
 file.
 GR It would be really nice that someone tell me about freezing the
 graphene
 GR sheet.
 GR thanks for any suggestion.




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[gmx-users] uninstallation- removing unknown files from bin

[Maryam Kowsar]

Dear users,

I want to uninstall gromacs. I used this command: rm -rf /usr/local/gromacs
and also removed some links that began with g_*** in the bin . however, I'm
not sure if the rest belong to gromacs or other programs also use them, and
should be deleted or not: completion.bash, completion.csh, completion.zsh,
demux.pl, GMXRC, GMXRC.bash, GMXRC.csh, GMXRC.zsh xplor2gmx.pl. Should all
of them be deleted?

thank you.
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Re: [gmx-users] filling a mesopore with water

[Maryam Kowsar]

Hi Chaban,
they are less than 5 Angstrom.


On Tue, Jun 23, 2015 at 1:30 AM, V.V.Chaban vvcha...@gmail.com wrote:

 what's the size of the hole?




 On Mon, Jun 22, 2015 at 11:37 AM, Maryam Kowsar maryam.kow...@gmail.com
 wrote:
  Dear users,
 
  I want to fill a mesoporous system with water or any other molecules or
  atoms. I tested genbox -cp .gro -cs spc216.gro -o but water molecules
 only
  surround the mespore not in the holes. Are there any commands in gromacs?
 
  thank you.
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[gmx-users] filling a mesopore with water

[Maryam Kowsar]

Dear users,

I want to fill a mesoporous system with water or any other molecules or
atoms. I tested genbox -cp .gro -cs spc216.gro -o but water molecules only
surround the mespore not in the holes. Are there any commands in gromacs?

thank you.
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Re: [gmx-users] Epsilon-rf

[Maryam Kowsar]

Dear Alex,
I have another question related to coulombtype selection. I dont want to
use pbc in my system so, PME and Ewald are not good choices. If I use
Reaction-field-zero and define a rcoulomb equal to my system size ( since
epsilon-rf is 0 out of cutoff size) would it do the same work as finding
epsilon-rf in generalized field reaction?
THANKS!

On Tue, Apr 28, 2015 at 10:22 PM, Maryam Kowsar maryam.kow...@gmail.com
wrote:

 If I use PME there's no need to find epsilon-rf, but I have to change some
 other parameters. I will try it.
 Thank you very much Alex!

 On Tue, Apr 28, 2015 at 11:31 AM, Alex nedoma...@gmail.com wrote:

  With reaction-field-zero, the only option is epsilon-rf=0. That aside,
 if the nanotube is small, i would use cut-off electrostatics with
 coulomb-cutoff comparable to the length of the tube.

 If the tube is long, I would use standard pme. I would be extremely
 careful about using truncated electrostatics in general. Given the above, I
 am not sure I understand what's there to calculate, unless you mean running
 a simulation and _obtaining_ a dielectric property as a result. In that
 case, given you system, it is a completely different discussion.


 Alex


 MK Not a poorly formed but a general question!

 MK You are right about reaction-field-zero. reaction-field leads to

 MK bad energy conservations. So, I decided to use reaction-field-zero

 MK but as I have some charges I don't know what to do with them. I

 MK have a CNT in which there are some ions. I want to calculate the

 MK epsilon-rf for it. I don't know if epsilon-rf belongs to the whole

 MK system and if so, how I should calculate it.

 MK thanks!




 MK On Tue, Apr 28, 2015 at 10:50 AM, Alex nedoma...@gmail.com wrote:

 MK That's a pretty poorly formed question, including the part where you

 MK actually calculate the epsilon-rf value. Can you please try again
 with

 MK a description of your system?


 MK Alex


 MK Dear all,

 MK I use reaction-field-zero as the coulombtype for my system. I wonder
 how I

 MK should choose the right epsilon-rf. How can I calculate the
 dielectric

 MK constant in the system?

 MK Thank you.









 --

 Best regards,

  Alexmailto:nedoma...@gmail.com
 nedoma...@gmail.com

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Re: [gmx-users] Epsilon-rf

[Maryam Kowsar]

If I use PME there's no need to find epsilon-rf, but I have to change some
other parameters. I will try it.
Thank you very much Alex!

On Tue, Apr 28, 2015 at 11:31 AM, Alex nedoma...@gmail.com wrote:

  With reaction-field-zero, the only option is epsilon-rf=0. That aside,
 if the nanotube is small, i would use cut-off electrostatics with
 coulomb-cutoff comparable to the length of the tube.

 If the tube is long, I would use standard pme. I would be extremely
 careful about using truncated electrostatics in general. Given the above, I
 am not sure I understand what's there to calculate, unless you mean running
 a simulation and _obtaining_ a dielectric property as a result. In that
 case, given you system, it is a completely different discussion.


 Alex


 MK Not a poorly formed but a general question!

 MK You are right about reaction-field-zero. reaction-field leads to

 MK bad energy conservations. So, I decided to use reaction-field-zero

 MK but as I have some charges I don't know what to do with them. I

 MK have a CNT in which there are some ions. I want to calculate the

 MK epsilon-rf for it. I don't know if epsilon-rf belongs to the whole

 MK system and if so, how I should calculate it.

 MK thanks!




 MK On Tue, Apr 28, 2015 at 10:50 AM, Alex nedoma...@gmail.com wrote:

 MK That's a pretty poorly formed question, including the part where you

 MK actually calculate the epsilon-rf value. Can you please try again
 with

 MK a description of your system?


 MK Alex


 MK Dear all,

 MK I use reaction-field-zero as the coulombtype for my system. I wonder
 how I

 MK should choose the right epsilon-rf. How can I calculate the dielectric

 MK constant in the system?

 MK Thank you.









 --

 Best regards,

  Alexmailto:nedoma...@gmail.com
 nedoma...@gmail.com

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[gmx-users] Epsilon-rf

[Maryam Kowsar]

Dear all,
I use reaction-field-zero as the coulombtype for my system. I wonder how I
should choose the right epsilon-rf. How can I calculate the dielectric
constant in the system?
Thank you.
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[gmx-users] how to calculate angles (molecules directions)

[Maryam Kowsar]

Dear users,
Is there a way in GROMACS to calculate the angle of each molecule with a
specified vector in each step?
Thank you in advance.
Regards,
--Maryam
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Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

[Maryam Kowsar]

Dear Christopher,

I will try the ways you mentioned. One of them should work! I wanted a
faster way than writing a code. However, if nothing works, I have to try
programming.at last.
Thanks a lot!

Cheers,
--Maryam

On Fri, Feb 13, 2015 at 8:51 AM, Christopher Neale 
chris.ne...@alum.utoronto.ca wrote:

 Sure.. hope it works. If not, then yes g_traj just gives you the
 positions, but you know the charges and you can compute the dipole
 yourself. I know, not an ideal solution, but I was just mentioning it since
 you may be forced to use it. Even better, write your own gromacs analysis
 tool by taking a very simple tool and re-purposing it. However, if you
 don't know C programming, then g_traj + awk can get you most any analyses
 that you need (though slowly).

 Chris.

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam
 Kowsar maryam.kow...@gmail.com
 Sent: 13 February 2015 00:19
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules
 directions)

 Dear Christopher,

 I tried g_traj -ox but it just gives me the positions not the orientations.
 I think I should try g_dipole.
 thank you very much!

 Cheers,
 --Maryam


 On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale 
 chris.ne...@alum.utoronto.ca wrote:

  Dear Maryam:
 
  I don't know. If g_dipoles doesn't give you what you want (and I have no
  idea if it will), then g_traj -ox will give you positions that you can
 then
  run a script over to compute things yourself. Probably somebody else can
  offer more advice here.
 
  Chris.
 
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam
  Kowsar maryam.kow...@gmail.com
  Sent: 12 February 2015 23:59
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules
  directions)
 
  Hi Christopher,
 
  You are on the right side! I mean the angle between the dipole moment
  vector of a molecule and a special vector (for a very simple assumption X
  axis for example). I found two options g_angle and g_sgangle but I think
  non of them can help. Are there any other commands to use?
  thank you!
 
  On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale 
  chris.ne...@alum.utoronto.ca wrote:
 
   How does one compute the angle between a vector and a molecule? I think
   you need to define your goal more completely.
  
   
   From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
   gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam
   Kowsar maryam.kow...@gmail.com
   Sent: 12 February 2015 23:45
   To: gromacs.org_gmx-users@maillist.sys.kth.se
   Subject: [gmx-users] Fwd: how to calculate angles (molecules
 directions)
  
   -- Forwarded message --
   From: Maryam Kowsar maryam.kow...@gmail.com
   Date: Fri, Feb 13, 2015 at 12:14 AM
   Subject: how to calculate angles (molecules directions)
   To: gromacs.org_gmx-users@maillist.sys.kth.se
  
  
   Dear users,
   Is there a way in GROMACS to calculate the angle of each molecule with
 a
   specified vector in each step?
   Thank you in advance.
   Regards,
   --Maryam
   --
   Gromacs Users mailing list
  
   * Please search the archive at
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   posting!
  
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[gmx-users] Fwd: how to calculate angles (molecules directions)

[Maryam Kowsar]

-- Forwarded message --
From: Maryam Kowsar maryam.kow...@gmail.com
Date: Fri, Feb 13, 2015 at 12:14 AM
Subject: how to calculate angles (molecules directions)
To: gromacs.org_gmx-users@maillist.sys.kth.se


Dear users,
Is there a way in GROMACS to calculate the angle of each molecule with a
specified vector in each step?
Thank you in advance.
Regards,
--Maryam
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Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

[Maryam Kowsar]

Dear Christopher,

I tried g_traj -ox but it just gives me the positions not the orientations.
I think I should try g_dipole.
thank you very much!

Cheers,
--Maryam


On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale 
chris.ne...@alum.utoronto.ca wrote:

 Dear Maryam:

 I don't know. If g_dipoles doesn't give you what you want (and I have no
 idea if it will), then g_traj -ox will give you positions that you can then
 run a script over to compute things yourself. Probably somebody else can
 offer more advice here.

 Chris.

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam
 Kowsar maryam.kow...@gmail.com
 Sent: 12 February 2015 23:59
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] Fwd: how to calculate angles (molecules
 directions)

 Hi Christopher,

 You are on the right side! I mean the angle between the dipole moment
 vector of a molecule and a special vector (for a very simple assumption X
 axis for example). I found two options g_angle and g_sgangle but I think
 non of them can help. Are there any other commands to use?
 thank you!

 On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale 
 chris.ne...@alum.utoronto.ca wrote:

  How does one compute the angle between a vector and a molecule? I think
  you need to define your goal more completely.
 
  
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam
  Kowsar maryam.kow...@gmail.com
  Sent: 12 February 2015 23:45
  To: gromacs.org_gmx-users@maillist.sys.kth.se
  Subject: [gmx-users] Fwd: how to calculate angles (molecules directions)
 
  -- Forwarded message --
  From: Maryam Kowsar maryam.kow...@gmail.com
  Date: Fri, Feb 13, 2015 at 12:14 AM
  Subject: how to calculate angles (molecules directions)
  To: gromacs.org_gmx-users@maillist.sys.kth.se
 
 
  Dear users,
  Is there a way in GROMACS to calculate the angle of each molecule with a
  specified vector in each step?
  Thank you in advance.
  Regards,
  --Maryam
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