[gmx-users] genion problem with topology

[gangotri dey]

Dear all,

I have replaced one water molecule in the solvent with a Cl atom using
genion. My syntax is as follows:

gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1
-nname CL

I have generated the ions.tpr using the ion.mdp file as in the tutorial
from Bevan group.
I see that the topol.top adds CL at the end under [molecules] but when I
try to minimize the geometry using the new solvate.gro file the error as
given as

ERROR 1 [file topol.top, line 37]:
  No such moleculetype CL

I do not understand how I can rectify the problem. Can someone help?

*Thank you*

*Gangotri Dey*
-- 
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.

Re: [gmx-users] conversion of a trajectory from .trr to .gro

[gangotri dey]

Dear Justin and Dash,

Thank you for the kind response.
I have another related problem. My xtc file is huge ~ 15 GB as I ran my
calculation for 5 ns in a big box. I can convert the .xtc to .gro but I
would like to do it in parallel using the cluster as it ran for a long time
when I used the head node.
However, when I use the below syntax and submit the job to the queue it is
asking for a group index that I do not know how to provide when using the
cluster to run the job.

gmx_mpi trjconv -s *.tpr -f *.xtc  -o conf.gro -sep

In this case, what should I do please?


*Thank you*

*Gangotri *




On Mon, Sep 18, 2017 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 9/18/17 4:18 PM, gangotri dey wrote:
>
>> Hello!
>>
>> I would save it in vmd all at once but I would like to ideally save it in
>> separate files. Also, the trajconv statement did not work.
>>
>>
> Your original error will be solved by passing a .tpr file to trjconv -s,
> as suggested below.  If you want to save intervals of time into separate
> files, use -b and -e.
>
> -Justin
>
>
>> *Thank you*
>>
>> *Gangotri *
>>
>>
>>
>>
>>
>> On Mon, Sep 18, 2017 at 3:08 PM, R C Dash <rcdash0...@gmail.com> wrote:
>>
>> Open you the gro file in VMD. Add load data and show the trr or xtc file.
>>> right click on to it and save coordinate. File type. gro.
>>> or
>>> trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro
>>>
>>> RC Dash,
>>>
>>>
>>> On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey <holyriv...@gmail.com>
>>> wrote:
>>>
>>> Dear all,
>>>>
>>>> I would like to transform my trajectory file n.trr or n.xtc to n.gro
>>>> after
>>>> my production run. I have used trjcat and trjconv to transform it using
>>>> the
>>>> index file. But in both the cases, it says "Can not write a gro file
>>>> without atom names". How can I transform it please?
>>>>
>>>>
>>>>
>>>> *Thank you*
>>>>
>>>> *Gangotri *
>>>> --
>>>> 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.
>>>>
>>>>
>>>
> --
> ==
>
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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.

Re: [gmx-users] gmx_mpi command line in version 5.1.4

[gangotri dey]

I hope your gromacs is compiled in a parallel cluster for you to use
gmx_mpi.



*Thank you*

*Gangotri *
On Tue, Sep 19, 2017 at 11:06 AM, K. Subashini 
wrote:

> Hi gromacs users,
>
>
> I am using version 5.1.4
>
>
> How to use gmx_mpi?
>
>
> I got the following error message
>
>
> Executable:   /home/subashini/GPU/bin/gmx_mpi
> Data prefix:  /home/subashini/GPU
> Command line:
>   gmx_mpi -v -deffnm eq
>
> ---
> Program: gmx_mpi, VERSION 5.1.4
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
> Unknown command-line option -v
> Unknown command-line option -deffnm
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> Halting program gmx_mpi
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --
>
>
> Kindly let me know how to fix it?
>
>
> Thanks,
>
> Subashini.K
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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.

Re: [gmx-users] conversion of a trajectory from .trr to .gro

[gangotri dey]

Hello!

I would save it in vmd all at once but I would like to ideally save it in
separate files. Also, the trajconv statement did not work.



*Thank you*

*Gangotri *





On Mon, Sep 18, 2017 at 3:08 PM, R C Dash <rcdash0...@gmail.com> wrote:

> Open you the gro file in VMD. Add load data and show the trr or xtc file.
> right click on to it and save coordinate. File type. gro.
> or
> trajconv -f xxx.trr or xtc -s xxx.tpr -o xxx.gro
>
> RC Dash,
>
>
> On Mon, Sep 18, 2017 at 2:42 PM, gangotri dey <holyriv...@gmail.com>
> wrote:
>
>> Dear all,
>>
>> I would like to transform my trajectory file n.trr or n.xtc to n.gro after
>> my production run. I have used trjcat and trjconv to transform it using
>> the
>> index file. But in both the cases, it says "Can not write a gro file
>> without atom names". How can I transform it please?
>>
>>
>>
>> *Thank you*
>>
>> *Gangotri *
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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.

[gmx-users] conversion of a trajectory from .trr to .gro

[gangotri dey]

Dear all,

I would like to transform my trajectory file n.trr or n.xtc to n.gro after
my production run. I have used trjcat and trjconv to transform it using the
index file. But in both the cases, it says "Can not write a gro file
without atom names". How can I transform it please?



*Thank you*

*Gangotri *
-- 
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.

[gmx-users] easy sampling of data

[gangotri dey]

Dear all,

I have a simulation that I ran for 5 ns. I have saved after every 0.1 ps. I
would like to extract the structure after every 1 ns.  Is there any easy
way to do it in gromacs?


*Thank you*

*Gangotri Dey*
-- 
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.

Re: [gmx-users] (no subject)

[gangotri dey]

Dear Alex and Mark,

Thank you for your kind reply.

To begin with I am a Postdoc but with expertise is in DFT. It is my first
venture into force field MD calculations. Hence, I am struggling. My group
and the boss has similar expertise. So we have turned to public forums to
ask questions.

My system is a brick floating in the water as you have correctly
identified.
My system is a periodic MnO2 surface. It has triclinic crystal system. I
want it to be solvated in all 3 directions but within the boundary of the
unit cell. This means that I do not want any water molecule between the
surface and its continuous periodic image. I want the water to be maximum
in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
insert_molecule and then -nmol and -ip option. But this still generates a
structure with water molecules beyond the desired x and y plane. I am not
sure how can I get this done as desired.

If the question and the problem are not very clear, please let me know. I
will try to reframe my words.

Looking forward to a healthy discussion.

Thank you
G.




*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 8:06 PM, Alex <nedoma...@gmail.com> wrote:

>
> I did not quite understand your comment.
>>>
>>> However, I am trying my best to answer it.
>>> I have a surface MnO2 model. I have solvated the structure in all 3
>>> directions. After that, I minimize it and run NVT simulation with the
>>> parameters as mentioned. However, I see that there is a deformation of
>>> the
>>> surface and it does not remain a flat surface. Instead, it curls like a
>>> ribbon. This should not be the case. Hence, I am wondering what are the
>>> factors that can lead to this deformation? Are the parameters in the NVT
>>> simulation good enough or else there is a problem that I cannot see.
>>>
>>> G
>>>
>>> There are a few points to be made...
> 1. The shape of your system, which is "solvated in all 3 directions" is
> very unclear. Is this a brick floating in water?
> 2. Please do not solvate anything until you have established that your
> "surface" is happy in vacuum.
> 3. If you have bending as a whole, it could be indicative of large
> internal strains, in which case NVT is probably a poor option. When you say
> you have "a surface MnO2 model," is it something like this?
> https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> e-dioxide-from-xtal-sheet-3D-balls.png
> 4. This community is mostly focused on biomolecular simulations and noone
> will be able to verify your parameterization of a solid crystal. Here is
> the rule of thumb though: If something bends when it shouldn't bend, your
> model is bad, which really has nothing to do with Gromacs.
> 5. If you are a student and points 1-4 aren't something your doctoral
> advisor already mentioned, maybe you should find another advisor.
>
> Alex
>
>
> Hi,
>>>>
>>>> Are you trying to implement a model that you know is capable of produce
>>>> a
>>>> surface that does not deform in unexpected ways?
>>>>
>>>> Mark
>>>>
>>>> On Mon, 7 Aug 2017 16:35 gangotri dey <holyriv...@gmail.com> wrote:
>>>>
>>>> Dear all,
>>>>>
>>>>> I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
>>>>> have solvated the surface with water in all 3 directions. After the NVT
>>>>> run, I see that the surface is deformed. I was wondering what else can
>>>>>
>>>> I
>>>
>>>> add in my nvt.mdp to not encounter this problem?
>>>>>
>>>>> I have mainly followed the examples in the forum for graphene/CNT
>>>>>
>>>> growth.
>>>
>>>> title   = MnO2  in H2O NVT equilibration
>>>>> ; Run parameters
>>>>> integrator  = md; leap-frog integrator
>>>>> nsteps  = 5 ; 2 * 50 = 100 ps
>>>>> dt  = 0.002 ; 2 fs
>>>>> ; Output control
>>>>> nstxout = 50; save coordinates every 0.10 ps
>>>>> nstvout = 50; save velocities every 0.10 ps
>>>>> nstenergy   = 50; save energies every 0.10 ps
>>>>> nstlog  = 50; update log file every 0.10 ps
>>>>> ; Bond parameters
>>>>> continuation= no 

Re: [gmx-users] (no subject)

[gangotri dey]

I did not quite understand your comment.

However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.

G



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 5:04 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Are you trying to implement a model that you know is capable of produce a
> surface that does not deform in unexpected ways?
>
> Mark
>
> On Mon, 7 Aug 2017 16:35 gangotri dey <holyriv...@gmail.com> wrote:
>
> > Dear all,
> >
> > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> > have solvated the surface with water in all 3 directions. After the NVT
> > run, I see that the surface is deformed. I was wondering what else can I
> > add in my nvt.mdp to not encounter this problem?
> >
> > I have mainly followed the examples in the forum for graphene/CNT growth.
> >
> > title   = MnO2  in H2O NVT equilibration
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 5 ; 2 * 50 = 100 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 50; save coordinates every 0.10 ps
> > nstvout = 50; save velocities every 0.10 ps
> > nstenergy   = 50; save energies every 0.10 ps
> > nstlog  = 50; update log file every 0.10 ps
> > ; Bond parameters
> > continuation= no; first dynamics run
> > constraint_algorithm= lincs ; holonomic constraints
> > constraints = none  ; all bonds (even heavy atom-H
> > bonds) constrained
> > lincs_iter  = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > cutoff-scheme   = Verlet
> > ns_type = grid  ; search neighboring grid cells
> > nstlist = 10; 20 fs, largely irrelevant with
> > Verlet
> > rcoulomb= 1.0   ; short-range electrostatic
> cutoff
> > (in nm)
> > rvdw= 1.0   ; short-range van der Waals
> cutoff
> > (in nm)
> > ; Electrostatics
> > coulombtype = PME   ; Particle Mesh Ewald for long-range
> > electrostatics
> > pme_order   = 4 ; cubic interpolation
> > fourierspacing  = 0.16  ; grid spacing for FFT
> > ; Temperature coupling is on
> > tcoupl  = V-rescale ; modified Berendsen
> thermostat
> > tc-grps = SOL MnO ; three coupling groups - more accurate
> > tau_t   = 0.1 0.1; time constant, in ps
> > ref_t   = 300 300; reference temperature, one for
> each
> > group, in K
> > ; Pressure coupling is off
> > pcoupl  = no; no pressure coupling in NVT
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > periodic-molecules = yes
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes   ; assign velocities from Maxwell
> > distribution
> > gen_temp= 300   ; temperature for Maxwell distribution
> > gen_seed= 18; generate a random seed
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > Postdoctoral Associate
> > Rutgers University New Brunswick
> > Chemistry and Chemical Biology
> > 174 Frelinghuysen Road, Piscataway, NJ 08854
> > Phone: +16092162254
> > --
> > 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

[gmx-users] solvate only in the z-direction

[gangotri dey]

Dear all,

I am working with MnO2 surface and I would like to solvate the surface only
in the z-direction. How best can I do it, please?

*Thank you*

*Gangotri Dey*
-- 
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.

[gmx-users] (no subject)

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can I
add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with
Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.0   ; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL MnO ; three coupling groups - more accurate
tau_t   = 0.1 0.1; time constant, in ps
ref_t   = 300 300; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
periodic-molecules = yes
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
-- 
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.

[gmx-users] MnO2 periodic system

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster periodic). After the
NVT run, I see that the surface is deformed. I was wondering what else can
I add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT growth.

title   = MnO2  in H2O NVT equilibration
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 50 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 50; save coordinates every 0.10 ps
nstvout = 50; save velocities every 0.10 ps
nstenergy   = 50; save energies every 0.10 ps
nstlog  = 50; update log file every 0.10 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = none  ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with
Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.0   ; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = SOL MnO ; three coupling groups - more accurate
tau_t   = 0.1 0.1; time constant, in ps
ref_t   = 300 300; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
periodic-molecules = yes
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= 18; generate a random seed



*Thank you*

*Gangotri Dey*
-- 
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.

Re: [gmx-users] Problem with dihedral restraints

[gangotri dey]

Thank you for the kind reply. I will compute and update in the post.



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Fri, Aug 4, 2017 at 10:31 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> You should expect changes, you're not freezing the angles in place. You're
> making it less energetically favourable for them to change. But if the
> environment is strong enough, they'll respond to that. Increase kfac by a
> factor of a thousand and they'll probably not move noticeably. Whether that
> is a good idea is something you might find out later :-)
>
> Mark
>
> On Fri, Aug 4, 2017 at 4:16 PM gangotri dey <holyriv...@gmail.com> wrote:
>
> > Hello!
> >
> > I posted a question a few days back and I got a reply but it still does
> not
> > work.
> >
> > I have a small drug molecule that I would like to compute. I want to
> > restraint the Ramachandran dihedral angles. I have used the following
> lines
> > in the .itp file for the molecule. It was suggested that I increase the
> > force constant, which I did. However, I still see the change in the
> > dihedral angles after the NVT, NPT and Production run. I am not sure how
> > best it can be implemented.
> >
> >
> >
> > [ dihedral_restraints ]
> > ; ai   ajakal  type  phi  dphi  kfac
> > 698 702 692 691 1 -142.56 0 100
> > 719 712 716 698 1 -84.24 0 100
> >
> > 702698716712 150.3766 0 100
> > 695691    692702 1  -166.8294 0 100
> >
> >
> > My .mdp file is similar to the one used in the Bevan lab tutorial online.
> >
> >
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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.

[gmx-users] Problem with dihedral restraints

[gangotri dey]

Hello!

I posted a question a few days back and I got a reply but it still does not
work.

I have a small drug molecule that I would like to compute. I want to
restraint the Ramachandran dihedral angles. I have used the following lines
in the .itp file for the molecule. It was suggested that I increase the
force constant, which I did. However, I still see the change in the
dihedral angles after the NVT, NPT and Production run. I am not sure how
best it can be implemented.



[ dihedral_restraints ]
; ai   ajakal  type  phi  dphi  kfac
698 702 692 691 1 -142.56 0 100
719 712 716 698 1 -84.24 0 100

702698716712 150.3766 0 100
695691692702 1  -166.8294 0 100


My .mdp file is similar to the one used in the Bevan lab tutorial online.




*Thank you*

*Gangotri Dey*
-- 
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.

[gmx-users] segmentation fault for unknown reason

[gangotri dey]

Hello!

I am trying to minimize a periodic MnO2 surface using UFF force fields. I
have previously computed many structures using MnO2 clusters. I did not
face much problem.

However, when I am trying to compute the minimization using the following
minim.mdp there is segmentation error as follows.

; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 1000.0; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 50; Frequency to update the
neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
coulombtype = PME   ; Treatment of long range
electrostatic interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions
(yes/no)


Error:

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot=  3.46301e+34 Fmax= 2.91045e+06, atom=
289
[fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error:
Segmentation fault (signal 11)
./script: line 5: 54036 Segmentation fault  (core dumped) gmx_mpi mdrun
-ntomp 1 -v -deffnm em

I do not understand this problem. Is there anything wrong with my structure
or the minim.mdp?



*Thank you*

*Gangotri Dey*
-- 
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.

Re: [gmx-users] protein -ligand complex dissociating during simulation

[gangotri dey]

Hey!

You might want to constrain the bond between the 2 protein chains.

G



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Fri, Jul 21, 2017 at 8:56 AM, Sneha Vishwanath <
snehavishwanat...@gmail.com> wrote:

> Dear all
>
> I am simulating a dimeric protein, with each subunit bound to a small
> molecule. During the simulation, one of the ligands is dissociating from
> the chain and moving all around the chain while the same ligand remains
> bound to the chain during simulation. Experiments show that the ligand
> binds to both the subunit which is further supported by the experimental
> structure of the protein-ligand complex (which I have used for the
> simulation). The simulation is for 50 ns and it usually starts dissociating
> after 10 ns.
>
> Any thoughts on why could it be happening and how it can be circumvented?
> Any help would be useful.
>
> Thanks in advance.
>
> Regards
> Sneha Vishwanath
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/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.

[gmx-users] dihedral restraint

[gangotri dey]

Hello all,

I am a relatively new user of gromacs. Hence, I am encountering some
problem.

I am studying few drug molecules onto a metal oxide surface. I would like
to constrain the Ramachandran angles. I am using gromacs version 5.4.0.

I have added the dihedral restraint angles in the itp file that reads as
follows.

[ dihedral_restraints ]
; ai   ajakal  type  phi  dphi  kfac
698 702 692 691 1 163.19 0 1
719 712 716 698 1 -84.24 0 1

712 716 698 689 1 -35.93 0 1
702 692 691 686 1 180.42 0 1

I have read in this forum that there is no need to add any more key words
like the previous version in the mdp file.


However, the dihedral angles are changing and I am not sure how to restrain
them.
Is there any part that I am missing.


*Thank you*

*Gangotri Dey*
-- 
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.