Re: [gmx-users] Trouble running simulations with Nitrogen

[Ali Ahmed]

Hi
Try this

http://erg.biophys.msu.ru/tpp/

Best

On Thu, Jul 19, 2018 at 10:54 PM, Joshua Cummings <
joshua.cummi...@uon.edu.au> wrote:

> Hi Everyone,
>
>
> I'm currently trying to run some simulations that involve the absorption
> of N2 into a liquid solvent. I'm having some difficulty in generating the
> topology for N2. For reference, the pdb file I have for N2 is as follows:
>
>
> HETATM1  N6B HDZ 0   0.000   0.000   0.553  1.00  0.00
>N
> HETATM2  N6A HDZ 0   0.000   0.000  -0.553  1.00  0.00
>N
> CONECT12
> CONECT21
> END
>
>
> When I try to generate the .itp file and topology via pdb2gmx (OPLS),
> gromacs doesn't recognise the residue. I've tried using both the LigParGen
> server and the PRODRG to generate the topology, but neither work. PRODRG
> generates an error saying it does not deal with mono/di-atomic molecules
> and LigParGen won't recognise N2 at all.
>
>
> I haven't had any trouble generating topologies for other small gas
> molecules such as CH4, am I missing something here or are OPLS parameters
> not possible for N2? Should I use some other forcefield for N2?
>
>
> Thanks in advance everyone,
>
>
> JOSHUA Cummings
>
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[gmx-users] Trouble running simulations with Nitrogen

[Joshua Cummings]

Hi Everyone,


I'm currently trying to run some simulations that involve the absorption of N2 
into a liquid solvent. I'm having some difficulty in generating the topology 
for N2. For reference, the pdb file I have for N2 is as follows:


HETATM1  N6B HDZ 0   0.000   0.000   0.553  1.00  0.00   N
HETATM2  N6A HDZ 0   0.000   0.000  -0.553  1.00  0.00   N
CONECT12
CONECT21
END


When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs 
doesn't recognise the residue. I've tried using both the LigParGen server and 
the PRODRG to generate the topology, but neither work. PRODRG generates an 
error saying it does not deal with mono/di-atomic molecules and LigParGen won't 
recognise N2 at all.


I haven't had any trouble generating topologies for other small gas molecules 
such as CH4, am I missing something here or are OPLS parameters not possible 
for N2? Should I use some other forcefield for N2?


Thanks in advance everyone,


JOSHUA Cummings

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[gmx-users] Calculate pore radius using water molecules

[Mijiddorj B]

Dear GMX users,

I would like to analyze a pore radius using the number of water molecules
inside it. I do not have any experience. How can I count water molecules
inside the pore? I want to get the time-dependent number of molecules
inside the pore.

Please advice me?


Best regards,

Miji
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[gmx-users] Compressing bundles of fibers into a surface

[paul buscemi]

Dear gmx users

I’m in the process of creating a PE polymer surface.

pdb and  itp files were obtained from ATB and were used to produce a   (xyz) 
142  x 6 x 60 A  box ( starting size ) with 300  150 A long molecules.

They were neatly aligned to start  and - using  pcoupletype = surface-tension 
and a restraint on the x direction ( fc=10) they stay aligned through md but 
are now in bundles - which is what they should do

But now I want to compress ( move them in the y direction ) the bundles into a 
142 x 6 x  say 20 A box. i.e. a  more or less complete surface

I’ve tried re-running npt on the first md result, with no change.  (10 ns md)  
Making a smaller box ( smaller y)  with confedit and running npt or md leads to 
very High PE.

Other than waiting for the cows to come home using md,, could a suggestion be 
made  to coerce the bundles to come together ?

regards
Paul
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[gmx-users] surface tension in free energy calculation

[Ali Shomali]

 Dear All,
I’m simulating a system of monolayer/water interface and I want to
calculate the change in the free energy (using Jarzynski method if
possible) of my system in the following process. First, my system box is
compressed to a certain size (by moving boundaries) and then it is expanded
again to the corresponding initial box size. How can I calculate the force?
Since I want to study the effect of surface tension on the free energy
variations and the surface tension is actually applied from the image of
monolayers from periodic boundaries.
Thank you for your kind helps
Ali
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Re: [gmx-users] Problems during installation

[Szilárd Páll]

On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan 
wrote:

> Hi Mark,
>
> Thank you for the quick answer. My group is experimenting with a GPU-heavy
> processor-light configuration similar to the Amber machines available from
> Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
> understanding, for this configuration to be successful performance-wise,
> gromacs would've to do all the calculating on GPUs, and not just
> electrostatics. That's why we're looking at openmm enabled versions.
>

For that you'd need the ~8 year old GROMACS 4.5 with OpenMM 2.x (IIRC)
support which is ancient and unsupported so really not a good idea.

Instead, use the latest release. Hardware-wise, ddeally you'd want to have
2-3 faster (wokstation) or 3-5 slower (server) cores per GPU for good
CPU-GPU balance.
--
Szilárd


> If you and others have alternate suggestions, we would be really eager to
> hear them. Thank you for your time.
>
> Regards,
> Rajat
>
> On Mon, 16 Jul 2018, 10:25 pm Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > This code was not ever functional in the 4.6 branch, so if you want it to
> > work, try 4.5.7. But really there is no reason to want to build it any
> more
> > - use the CUDA and OpenCL ports available in more recent GROMACS.
> >
> > Mark
> >
> > On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan 
> > wrote:
> >
> > > Dear all,
> > > I'm trying to install openmm enabled version of gromacs 4.6.7 on a
> 6-core
> > > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> > > strange error while running make:
> > >
> > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> > ‘cmain’:
> > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> > > missing braces around initializer [-Wmissing-braces]
> > >gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> > >^
> > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note:
> (near
> > > initialization for ‘hw_opt’)*
> > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> > > ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’;
> did
> > > you mean ‘gpu_opt’?*
> > > * { "-gpu_id",  FALSE, etSTR, {_opt.gpu_id},*
> > >  ^
> > > src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> > > 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> > > make[2]: ***
> > [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> > > Error 1
> > > CMakeFiles/Makefile2:1902: recipe for target
> > > 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> > > make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> > > Makefile:162: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > > I have installed cuda 9.1, openmm, fftw, open-mpi and all other
> necessary
> > > software, so I'm at a loss. Please help me out. Google did not have
> much
> > > leads.
> > >
> > > Thank you.
> > >
> > > Regards,
> > > Rajat
> > >
> > > --
> > > Dr. Rajat Desikan (Post Doctoral Fellow)
> > > Prof. Narendra M Dixit's Lab (no 1),
> > > Dept. of Chemical Engineering,
> > > Indian Institute of Science, Bangalore
> > > --
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Re: [gmx-users] CNT md simulation & unusual minimized structure

[Justin Lemkul]

On 7/19/18 7:08 AM, Atila Petrosian wrote:

Dear gromacs users,

I am doing md simulation of cnt + drug (lig) + water molecules.



I get lig.gro and lig.itp files using antechamber module and amb2gmx script.



I used cnt force field parameters from paper
(*https://pubs.acs.org/doi/abs/10.1021/jp011344u
*)



I get pdb file of cnt from nanotube modeller: (18,0), (Length = 34.468 Angstrom)



gmx_mpi editconf -f cnt.pdb -o cnt.gro -c -box 8 8 3.4468



gmx_mpi x2top -f cnt.gro -o cnt.top -ff cnt -name CNT -pbc -noparam



I merged gro files and itp and top files without problem.





gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o em_vac.tpr



gmx_mpi mdrun -v -deffnm em_vac -nb gpu >& em_vac.job &



gro file after energy minimization is unusual.



https://1drv.ms/u/s!AveJH4Y30cH0sQnyV-5RoaqhaeFJ


It looks like your box fits the CNT exactly and does not leave enough 
space for bonds between images, so you get distortion at the "ends" of 
the central image.


-Justin






lig.itp, topol.top and cnt.ff is as follows, respectively:



https://1drv.ms/u/s!AveJH4Y30cH0sHioMbu0GT2BDATg



https://1drv.ms/u/s!AveJH4Y30cH0sHrSTs-0f0kK-mE5



https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde





Please guide me to resolve this problem.


Best,

Atila


--
==

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] energy minimization_note

[Justin Lemkul]

On 7/19/18 6:18 AM, Atila Petrosian wrote:

Dear Mark,

Thanks for your answer.

“But typically EM in vacuum is short enough you should not consider

optimizing it.”. You are right. Using the reference manual about PME,

I created new mdp file as follows:



integrator   = steep

nsteps   = 5

emtol= 10

emstep   = 0.01

ns_type  = grid

rlist= 0.9

coulombtype  = PME

Cutoff-scheme= Verlet

vdwtype  = Cut-off

rcoulomb = 0.9

rvdw = 0.9

constraints  = none

periodic_molecules   = yes

fourierspacing   = 4

ewald_rtol   = 1e-5



This time I have not previous note in grompp command.


You shouldn't hack at cutoff values to try to improve performance. 
Cutoffs are part of the force field. As Mark said, performance in energy 
minimization is usually not of much importance, but even if you see this 
note in preparing your MD simulations, you shouldn't just play with 
settings to try to make things run faster.


-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] Ionic bonds

[Momin Ahmad]

Hello,

is there a difference in the implementation of an ionic bond and a 
covalent bond? For example UFF gives parameters for both atoms i and j. 
The atoms i and j should form an ionic bond and UFF gives me the 
parameters for the strecthing and bending potential. But in the case of 
dihedrals i only have information for sp^2 and sp^3 bonds. So should i 
just take the i and j as a sp^2 bond because i have the parameters for 
it (there are no parameters for a sp^3 )?


Cheers,
Momin

--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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[gmx-users] CNT md simulation & unusual minimized structure

[Atila Petrosian]

Dear gromacs users,

I am doing md simulation of cnt + drug (lig) + water molecules.



I get lig.gro and lig.itp files using antechamber module and amb2gmx script.



I used cnt force field parameters from paper
(*https://pubs.acs.org/doi/abs/10.1021/jp011344u
*)



I get pdb file of cnt from nanotube modeller: (18,0), (Length = 34.468 Angstrom)



gmx_mpi editconf -f cnt.pdb -o cnt.gro -c -box 8 8 3.4468



gmx_mpi x2top -f cnt.gro -o cnt.top -ff cnt -name CNT -pbc -noparam



I merged gro files and itp and top files without problem.





gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o em_vac.tpr



gmx_mpi mdrun -v -deffnm em_vac -nb gpu >& em_vac.job &



gro file after energy minimization is unusual.



https://1drv.ms/u/s!AveJH4Y30cH0sQnyV-5RoaqhaeFJ





lig.itp, topol.top and cnt.ff is as follows, respectively:



https://1drv.ms/u/s!AveJH4Y30cH0sHioMbu0GT2BDATg



https://1drv.ms/u/s!AveJH4Y30cH0sHrSTs-0f0kK-mE5



https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde





Please guide me to resolve this problem.


Best,

Atila
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[gmx-users] energy minimization_note

[Atila Petrosian]

Dear Mark,

Thanks for your answer.

“But typically EM in vacuum is short enough you should not consider

optimizing it.”. You are right. Using the reference manual about PME,

I created new mdp file as follows:



integrator   = steep

nsteps   = 5

emtol= 10

emstep   = 0.01

ns_type  = grid

rlist= 0.9

coulombtype  = PME

Cutoff-scheme= Verlet

vdwtype  = Cut-off

rcoulomb = 0.9

rvdw = 0.9

constraints  = none

periodic_molecules   = yes

fourierspacing   = 4

ewald_rtol   = 1e-5



This time I have not previous note in grompp command.
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[gmx-users] Segmentation fault and PCA Analysis

[Ahmed Mashaly]

Dear users,
I am trying to align my trajectory to an average structure pdb, the problem is 
that I have "Segmentation fault (core dumped)" while taking this pdb as a 
reference structure, while it worked with the em.tpr file ... I also tried to 
extract the pdb from the that em.tpr using gmx editconf and when I used it as a 
reference I faced the same problem, so I guess the peoblem with the pdb format 
... Any suggestions?
Another question about PCA, is there a way to do dot product in GROMACS?
Kind regards,Ahmed
 

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