Re: [gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

Hi Justin,
I actually want to scale the box (both moving the chains apart and close to
each other by changing the a and b parameters of the cell). I don't want to
run any dynamics at this point as I have already done quantum mechanics
minimization on this structure. When I use the editconf command the cell
parameters change but the coordinates of the atoms remain unchanged, i.e.
by compression the polymer chains remain outside of the cell... I was
wondering if editconf could scale the coordinates proportionally with the
cell parameters without distorting the bonds lengths?

gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686
1.9724 -angles 90.00 126.91 90.00

The original cell parameters are:
a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91,
gamma: 90.00

The unit cell consists of 4 polymer chains, each chain having 7 repeating
(C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds,
340 angles and 376 dihedrals.

Best
Maryam




On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul  wrote:

>
>
> On 4/3/20 11:16 PM, Maryam Sadeghi wrote:
> > Hi Salman,
> >
> > Tnx for the info, I actually want to do the cold-compression on my
> > crystalline structure. So basically I need to both compress and expand
> the
> > a and b parameters of the unit cell (the c parameter is already
> > optimized)... so it's not just building a supercell, but rather scaling
> > only 2 parameters of the unit cell simultaneously while remaping the new
> > coordinates inside the scaled cell... could "gmx  genconf -nbox ... ...
> > ..." handle this?
>
> It sounds like you need to actually perform a simulation in which high
> pressure is applied to compress the box. genconf is for duplicating a
> box N times in each dimension, and while you can change box vectors and
> scale coordinates with editconf (-scale option), this is not the same as
> compressing them and bond lengths, etc. will become distorted.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

Hi Salman,

Tnx for the info, I actually want to do the cold-compression on my
crystalline structure. So basically I need to both compress and expand the
a and b parameters of the unit cell (the c parameter is already
optimized)... so it's not just building a supercell, but rather scaling
only 2 parameters of the unit cell simultaneously while remaping the new
coordinates inside the scaled cell... could "gmx  genconf -nbox ... ...
..." handle this?

Best
Maryam


On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini 
wrote:

> Hi Maryam,
>
> The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I
> am just not sure if it could handle a triclinic cell.
> Since your unit cell is not that large, you even can use Avogadro or
> ASE-gui which both are good molecule editors and visualizers.
>
> Cheers,
> Salman
>
> On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi  >
> wrote:
>
> > Dear All,
> >
> > I need to scale the a and b parameters of a triclinic crystalline unit
> > cell. When I use the editconf command, only the cell parameters are
> scaled
> > while the coordinates of atoms are not remapped in the new cell.
> >
> > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560
> 0.5686
> > 1.9724 -angles 90.00 126.91 90.00
> >
> > The unit cell consists of 4 polymer chains, each chain having 7 repeating
> > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192
> bonds,
> > 340 angles and 376 dihedrals.
> >
> > The original cell parameters are:
> > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91,
> > gamma: 90.00
> >
> > Any suggestions how I can remap the coordinates (keeping the bonds and
> > angles constant) together with scaling the box?
> >
> > Thanks,
> > --
> > Gromacs Users mailing list
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[gmx-users] Scale Triclinic Box

[Maryam Sadeghi]

Dear All,

I need to scale the a and b parameters of a triclinic crystalline unit
cell. When I use the editconf command, only the cell parameters are scaled
while the coordinates of atoms are not remapped in the new cell.

gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686
1.9724 -angles 90.00 126.91 90.00

The unit cell consists of 4 polymer chains, each chain having 7 repeating
(C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds,
340 angles and 376 dihedrals.

The original cell parameters are:
a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91,
gamma: 90.00

Any suggestions how I can remap the coordinates (keeping the bonds and
angles constant) together with scaling the box?

Thanks,
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[gmx-users] Converting Charmm to gmx format using cgenff

[Maryam]

Dear gmx users,

I am trying to generate topology for small ligands using cgenff . I will
like to confirm if the Charmm to gmx script available on the Mackerell
website is compatible with all versions of charmm forcefield or can only
be used with Charm36 forcefield. P.S. I have tried it with charm22* and
did not get any error, I will just like to double check.  Looking
forward to your reply.

Best regards,

Maryam





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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Re: [gmx-users] largest charge group

[Maryam Sadeghi]

Thank you very much Justin.

Just to confirm, in case of longer polymers can I assign 1 monomer/bead to
different charge groups?

Maryam

On Mon, Dec 30, 2019, 5:32 AM Justin Lemkul  wrote:

>
>
> On 12/30/19 2:53 AM, Maryam Sadeghi wrote:
> > Dear All,
> >
> > I have created a coarse-grain (cg) structure of a polymer containing 49
> > beads (the atomistic structure contains 193 atoms), each beads has a zero
> > charge.
> > I have created the .itp file manually, defining the atom types and the
> > bonds  and angles (no dihedrals in my model). When I used GROMAC's grompp
> > command, I get the following error:
> >
> > gmx grompp -f em.mdp -c cg_PCL_box.gro -p topol.top -o em.tpr -maxwarn 1
> >
> > Fatal error:
> > The largest charge group contains 49 atoms. The maximum is 32.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > Could anyone suggest how I can fix this problem? I will need to do
> > simulations on longer chains as well.
>
> Assign different residues/monomers to different charge groups. Your
> entire polymer is one group, which is not allowed.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] largest charge group

[Maryam Sadeghi]

Dear All,

I have created a coarse-grain (cg) structure of a polymer containing 49
beads (the atomistic structure contains 193 atoms), each beads has a zero
charge.
I have created the .itp file manually, defining the atom types and the
bonds  and angles (no dihedrals in my model). When I used GROMAC's grompp
command, I get the following error:

gmx grompp -f em.mdp -c cg_PCL_box.gro -p topol.top -o em.tpr -maxwarn 1

Fatal error:
The largest charge group contains 49 atoms. The maximum is 32.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Could anyone suggest how I can fix this problem? I will need to do
simulations on longer chains as well.

Thank you
Maryam
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[gmx-users] Time step mismatch.

[Maryam]

Dear gmx users,

I have two xtc files generated from my simulation with two different
time steps. I had to change the time step/mdp options because of disc
size. After the simulation, I tried to use trjcat to combine the two xtc
files so I can perform analsis on the trajectory. But I get this warning  :

Timesteps at t=1.4028e+07 don't match (1200, 1500), How do I fix this?
is it possible to rewrite the time step after the simulation?Thanks in
advance.

Best regards,

Maryam





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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[gmx-users] Iterative Boltzman Inversion

[Maryam Sadeghi]

Dear All,

I was wondering if there are any codes in GROMACS for doing Iterative
Boltzman Inversion to reproduce the target pair distribution functions for
a MARTINI coarse grained structure given by atomistic simulations?

Best
Maryam
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[gmx-users] Average RDF

[Maryam Sadeghi]

Hi All,

I am simulating a single chain of Polyethylene Glycol (PEG9 terminating
with -OH groups) in water, and I need to calculate the RDF for the terminal
Oxygens & O-water (Ot-Ow) as well as the ether Oxygens within the chain (in
my case 9 Oxygens) and O-water (Oe-Ow).
I have calculated the Oe-Ow RDF for each single O within the chain, but I
am actually looking for the average RDF of all ether Oxygens. Could anyone
tell me how I can compute an average RDF in GROMACS for all the ether
Oxygens within the chain?

Thank you
Maryam
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[gmx-users] Average RDF

[Maryam Sadeghi]

Hi All,

I am simulating a single chain of Polyethylene Glycol (PEG9 terminating
with -OH groups) in water, and I need to calculate the RDF for the terminal
Oxygens & O-water as well as the ether Oxygens within the chain (in my case
9 Oxygens) and O-water.
I have calculated the Oe-Ow RDF for each single O within the chain, but I
am actually looking for the average RDF of all ether Oxygens. Could anyone
tell me how I can compute an average RDF in GROMACS for all the ether
Oxygens within the chain and O-water in 1 single graph?

Thank you
-- 

Maryam S. Sadeghi
P *Please think before printing*
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[gmx-users] gromacs.org_gmx-users@maillist.sys.kth.se; jalem...@vt.edu

[Maryam Sadeghi]

 Hi All,

I have created a crystal structure of 2 polymer chains (PEG) and I need to
calculate the cohesive energy for my system using CHARMM36 FF. In this case
my fix_mol2 file includes 2 ligands, to convert to str file I get the
following error:

readmol2 warning: non-unique atoms were renamed. Now processing molecule
LIG ... attype warning: carbon radical, carbocation or carbanion not
supported; skipped molecule.

How can I fix this problem? Changing the ligand IDs and names does not
help. I even tried to make 2 separate mol2 files for each chain in the
crystal structure, but still get the same error while converting to str
file...


-- 

Maryam S. Sadeghi
P *Please think before printing*
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[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

[Maryam Sadat Sadeghi]

Hi All,

I have created a crystal structure of 2 polymer chains (PEG) and I need to 
calculate the cohesive energy for my system using CHARMM36 FF. In this case my 
fix_mol2 file includes 2 ligands, to convert to str file I get the following 
error:

readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG 
... attype warning: carbon radical, carbocation or carbanion not supported; 
skipped molecule.

How can I fix this problem? Changing the ligand IDs and names does not help. I 
even tried to make 2 separate mol2 files for each chain in the crystal 
structure, but still get the same error while converting to str file...

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[gmx-users] How to generate CHARMM force field for GROMACS using CGenFF for polymer crystal structure?

[Maryam Sadat Sadeghi]

Hi All,

I have created a crystal structure of 2 polymer chains (PEG) and I need to 
calculate the cohesive energy for my system using CHARMM36 FF. In this case my 
fix_mol2 file includes 2 ligands, to convert to str file I get the following 
error:

readmol2 warning: non-unique atoms were renamed. Now processing molecule LIG 
... attype warning: carbon radical, carbocation or carbanion not supported; 
skipped molecule.

How can I fix this problem? Changing the ligand IDs and names does not help. I 
even tried to make 2 separate mol2 files for each chain in the crystal 
structure, but still get the same error while converting to str file...

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Re: [gmx-users] best performance on GPU

[Maryam]

Hi Paul
How can I run it on multiple nodes?
Thanks

On Fri., Aug. 2, 2019, 6:10 p.m. Paul Buscemi,  wrote:

> Why run moo on a single node ?
>
> PB
>
> > On Aug 1, 2019, at 5:53 PM, Mark Abraham 
> wrote:
> >
> > Hi,
> >
> > We can't tell whether or what the problem is without more information.
> > Please upload your .log file to a file sharing service and post a link.
> >
> > Mark
> >
> >> On Fri, 2 Aug 2019 at 01:05, Maryam  wrote:
> >>
> >> Dear all
> >> I want to run a simulation of approximately 12000 atoms system in
> gromacs
> >> 2016.6 on GPU with the following machine structure:
> >> Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
> >> support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
> >> instructions: AVX2_256 FFT library:
> >> fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
> >> support: enabled Hwloc support: disabled Tracing support: disabled Built
> >> on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE]
> Build
> >> OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
> >> brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23
> Model: 1
> >> Stepping: 1
> >> Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
> >> 7.5, ECC: no, stat: compatible
> >> i used different commands to get the best performance and i dont know
> which
> >> point i am missing. the quickest time possible is got by this
> command:gmx
> >> mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
> >> which is 10 ns/day! and it takes 2 months to end.
> >> though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin
> on
> >> -resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
> >> -append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
> >> with this properties I should be able to run it in  295 ns/day!
> >> could you help me find out what point i am missing that i can not reach
> the
> >> best performance level?
> >> Thank you
> >> --
> >> --
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Re: [gmx-users] best performance on GPU

[Maryam]

Hi Mark
here is the link to md.log:
https://www.dropbox.com/s/4fuu5g68nwwzys4/MD.log?dl=0
Thank you!


On Thu, Aug 1, 2019 at 6:54 PM Mark Abraham 
wrote:

> Hi,
>
> We can't tell whether or what the problem is without more information.
> Please upload your .log file to a file sharing service and post a link.
>
> Mark
>
> On Fri, 2 Aug 2019 at 01:05, Maryam  wrote:
>
> > Dear all
> > I want to run a simulation of approximately 12000 atoms system in gromacs
> > 2016.6 on GPU with the following machine structure:
> > Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
> > support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
> > instructions: AVX2_256 FFT library:
> > fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
> > support: enabled Hwloc support: disabled Tracing support: disabled Built
> > on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE]
> Build
> > OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
> > brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23
> Model: 1
> > Stepping: 1
> > Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
> > 7.5, ECC: no, stat: compatible
> > i used different commands to get the best performance and i dont know
> which
> > point i am missing. the quickest time possible is got by this command:gmx
> > mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
> > which is 10 ns/day! and it takes 2 months to end.
> >  though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin
> on
> > -resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
> > -append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
> > with this properties I should be able to run it in  295 ns/day!
> > could you help me find out what point i am missing that i can not reach
> the
> > best performance level?
> > Thank you
> > --
> > --
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[gmx-users] best performance on GPU

[Maryam]

Dear all
I want to run a simulation of approximately 12000 atoms system in gromacs
2016.6 on GPU with the following machine structure:
Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
instructions: AVX2_256 FFT library:
fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
support: enabled Hwloc support: disabled Tracing support: disabled Built
on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE] Build
OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23 Model: 1
Stepping: 1
Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
7.5, ECC: no, stat: compatible
i used different commands to get the best performance and i dont know which
point i am missing. the quickest time possible is got by this command:gmx
mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
which is 10 ns/day! and it takes 2 months to end.
 though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin on
-resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
-append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
with this properties I should be able to run it in  295 ns/day!
could you help me find out what point i am missing that i can not reach the
best performance level?
Thank you
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[gmx-users] space dependent electric field

[Maryam]

Dear all,

I want to apply a space but not time dependent electric field to my system.
I reviewed the source code of the electric field but it only has constant
and time dependent EF (pulsed EF). Can anyone help me find out how I can
change the source code to have space dependent EF without changing the
defined parameters in gromacs so that I wont face the problem of changing
all related subroutines? Which routines should I apply required changes if
I want to add some new parameters for the space dependent EF?
Thank you
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Re: [gmx-users] gmx mdrun with gpu

[Maryam]

Hello Reza
Yes I complied it with GPU and the version of CUDA is 9.1. Any suggestions?
Thanks.

On Sat., May 4, 2019, 1:45 a.m. Reza Esmaeeli, 
wrote:

> Hello Maryam,
> Have you compiled the gromacs 2019 with GPU?
> What version of CUDA do you have?
>
> - Reza
>
> On Saturday, May 4, 2019, Maryam  wrote:
>
> > Dear all,
> > I want to run a simulation in gromacs 2019 on a system with 1 gpu and 32
> > threads. I write this command: gmx mdrun -s md.tpr -v -nb gpu but it
> seems
> > it does not recognize gpus and it takes long for the simulation to reach
> > its end (-ntmpi ntomp and nt seem not working either). In gromacs 2016
> with
> > 2 gpus, I use gmx_mpi -s md.tpr -v -gpu_id 1 -nb gpu -ntomp 16 -pin on
> > -tunepme and it works fine, but the same command regardless of (gpu_id)
> > does not work in gromacs 2019. What flags should I use to get the best
> > performance of the simulation?
> > Thank you.
> > --
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[gmx-users] gmx mdrun with gpu

[Maryam]

Dear all,
I want to run a simulation in gromacs 2019 on a system with 1 gpu and 32
threads. I write this command: gmx mdrun -s md.tpr -v -nb gpu but it seems
it does not recognize gpus and it takes long for the simulation to reach
its end (-ntmpi ntomp and nt seem not working either). In gromacs 2016 with
2 gpus, I use gmx_mpi -s md.tpr -v -gpu_id 1 -nb gpu -ntomp 16 -pin on
-tunepme and it works fine, but the same command regardless of (gpu_id)
does not work in gromacs 2019. What flags should I use to get the best
performance of the simulation?
Thank you.
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[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] rdf calculation with respect to center of mass

[Maryam Khalkhali]

Dear gmx-users,

The radial distribution function with respect to center-of-mass was computable 
in old gromacs versions. How can I calculate that  in newer version(2016)?
Thanks in advance.

Maryam
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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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>>>>
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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
> > >> >>
> > >> >> * 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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> > >> 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
>>
>> * 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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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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[gmx-users] CNT in water

[maryam haji]

Dear Users,

I want to simulate CNT in water solvent with CHARMM27 force field. The used
parameters for simulation of CNT follows:



The .n2t file is:



CCA0.0012.011  3C 0.141   C 0.141   C 0.141

CCA0.0012.011  2C 0.141   C 0.141



The cntbonded.itp is:

[ bondtypes ]

; i j   func b0kb

CA  CA   3  0.1418   47890.0   21.867



[ angletypes ]

; i j   k  func th0   cth   ub0  cub

CA  CA  CA  2  120.00 562.20



[ dihedraltypes ]

; i j   k  l   func phi0 cp
mult

CA  CA  CA  CA  5  0.00 25.12 0.00 0.00

The cntnonbonded.itp is:

[ atomtypes ]

nameat.num masscharge  ptype   sigma   epsi

CA  6  12.01100 0.00 A 0.385   0.4396









The flexible SPC water model is used for simulation of water. The used
parameters for simulation of water are (spc_cnt.itp):



[ moleculetype ]

molname  nrexcl

SOL2

[ atoms ]

 nr   type  resnr residue  atom   cgnr charge   mass

 1 OW   1SOL OW  1  -0.82

 2 HW   1SOLHW1  1   0.41

 3 HW   1SOLHW2  1   0.41



#ifndef FLEXIBLE

[ settles ]

OW functdoh  dhh

1  1  0.1   0.16330



[ exclusions ]

1  2  3

2  1  3

3  1  2

#else

[ bonds ]

 i  j   functlength  force.c.

1  2  1  0.1   4637000.1 463700

1  3  1  0.1   4637000.1 463700



[ angles ]

 i  j   k  functangleforce.c.

2  1  3  1  109.47 383  109.47 383

#endif

I have a question:

I don’t know how to use the parameters of the Lennard-Jones potential, ɛCO
and *σ*CO for calculating interaction between water molecules and carbon in
nanotube in this simulation?



Thank you for any help
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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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>>> 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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[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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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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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
   http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
   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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* Please search the archive at 
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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
  --
  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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[gmx-users] Calculate heat capacity

[maryam haji]

Dear gromacs users

My system contains protein(15 residue) and CNT and water molecules and ion.

at the end of .top file is
[ molecules ]
; Compound#mols
Protein_chain_A 1
CNT 1
SOL  6531
NA  2

I want to calculate the heat capacity in ensemble NVT.outputs g_energy are:

---
  1  G96Angle 2  U-B  3  Proper-Dih.  4
 Fourier-Dih.
  5  Improper-Dih.6  CMAP-Dih.7  LJ-148  Coulomb-14

  9  LJ-(SR) 10  Coulomb-(SR)11  Coul.-recip.12
 Position-Rest.
 13  Potential   14  Kinetic-En. 15  Total-Energy16
 Conserved-En.
 17  Temperature 18  Pressure19  Constr.-rmsd20  Vir-XX

 21  Vir-XY  22  Vir-XZ  23  Vir-YX  24  Vir-YY

 25  Vir-YZ  26  Vir-ZX  27  Vir-ZY  28  Vir-ZZ

 29  Pres-XX 30  Pres-XY 31  Pres-XZ 32  Pres-YX

 33  Pres-YY 34  Pres-YZ 35  Pres-ZX 36  Pres-ZY

 37  Pres-ZZ 38  #Surf*SurfTen

 39  Coul-SR:Protein-Protein 40  LJ-SR:Protein-Protein

 41  Coul-14:Protein-Protein 42  LJ-14:Protein-Protein

 43  Coul-SR:Protein-CNT 44  LJ-SR:Protein-CNT

 45  Coul-14:Protein-CNT 46  LJ-14:Protein-CNT

 47  Coul-SR:Protein-SOL 48  LJ-SR:Protein-SOL

 49  Coul-14:Protein-SOL 50  LJ-14:Protein-SOL

 51  Coul-SR:Protein-NA  52  LJ-SR:Protein-NA

 53  Coul-14:Protein-NA  54  LJ-14:Protein-NA

 55  Coul-SR:CNT-CNT 56  LJ-SR:CNT-CNT

 57  Coul-14:CNT-CNT 58  LJ-14:CNT-CNT

 59  Coul-SR:CNT-SOL 60  LJ-SR:CNT-SOL

 61  Coul-14:CNT-SOL 62  LJ-14:CNT-SOL

 63  Coul-SR:CNT-NA  64  LJ-SR:CNT-NA65  Coul-14:CNT-NA  66
 LJ-14:CNT-NA
 67  Coul-SR:SOL-SOL 68  LJ-SR:SOL-SOL

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

 71  Coul-SR:SOL-NA  72  LJ-SR:SOL-NA73  Coul-14:SOL-NA  74
 LJ-14:SOL-NA
 75  Coul-SR:NA-NA   76  LJ-SR:NA-NA 77  Coul-14:NA-NA   78
 LJ-14:NA-NA
 79  T-Protein_CNT   80  T-Water_Ion

 81  Lamb-Protein_CNT82  Lamb-Water_Ion


when i select 1517 i have a warning that include:

WARNING: nmol = 1, this may not be what you want.

i konw that nmol is the number of molecules.i have two question

1-how can i calculate nmol?

2-Is nmol=mol water+mol cnt+mol protein?

Thanks in advance
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[gmx-users] Calculate heat capacity

[maryam haji]

Dear gromacs users

My system contains protein(15 residue) and CNT and water molecules and ion.

at the end of .top file is
[ molecules ]
; Compound#mols
Protein_chain_A 1
CNT 1
SOL  6531
NA  2

I want to calculate the heat capacity in ensemble NVT.outputs g_energy are:

---
  1  G96Angle 2  U-B  3  Proper-Dih.  4
 Fourier-Dih.
  5  Improper-Dih.6  CMAP-Dih.7  LJ-148  Coulomb-14

  9  LJ-(SR) 10  Coulomb-(SR)11  Coul.-recip.12
 Position-Rest.
 13  Potential   14  Kinetic-En. 15  Total-Energy16
 Conserved-En.
 17  Temperature 18  Pressure19  Constr.-rmsd20  Vir-XX

 21  Vir-XY  22  Vir-XZ  23  Vir-YX  24  Vir-YY

 25  Vir-YZ  26  Vir-ZX  27  Vir-ZY  28  Vir-ZZ

 29  Pres-XX 30  Pres-XY 31  Pres-XZ 32  Pres-YX

 33  Pres-YY 34  Pres-YZ 35  Pres-ZX 36  Pres-ZY

 37  Pres-ZZ 38  #Surf*SurfTen

 39  Coul-SR:Protein-Protein 40  LJ-SR:Protein-Protein

 41  Coul-14:Protein-Protein 42  LJ-14:Protein-Protein

 43  Coul-SR:Protein-CNT 44  LJ-SR:Protein-CNT

 45  Coul-14:Protein-CNT 46  LJ-14:Protein-CNT

 47  Coul-SR:Protein-SOL 48  LJ-SR:Protein-SOL

 49  Coul-14:Protein-SOL 50  LJ-14:Protein-SOL

 51  Coul-SR:Protein-NA  52  LJ-SR:Protein-NA

 53  Coul-14:Protein-NA  54  LJ-14:Protein-NA

 55  Coul-SR:CNT-CNT 56  LJ-SR:CNT-CNT

 57  Coul-14:CNT-CNT 58  LJ-14:CNT-CNT

 59  Coul-SR:CNT-SOL 60  LJ-SR:CNT-SOL

 61  Coul-14:CNT-SOL 62  LJ-14:CNT-SOL

 63  Coul-SR:CNT-NA  64  LJ-SR:CNT-NA65  Coul-14:CNT-NA  66
 LJ-14:CNT-NA
 67  Coul-SR:SOL-SOL 68  LJ-SR:SOL-SOL

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

 71  Coul-SR:SOL-NA  72  LJ-SR:SOL-NA73  Coul-14:SOL-NA  74
 LJ-14:SOL-NA
 75  Coul-SR:NA-NA   76  LJ-SR:NA-NA 77  Coul-14:NA-NA   78
 LJ-14:NA-NA
 79  T-Protein_CNT   80  T-Water_Ion

 81  Lamb-Protein_CNT82  Lamb-Water_Ion


when i select 1517 i have a warning that include:

WARNING: nmol = 1, this may not be what you want.

i konw that nmol is the number of molecules.i have two question

1-how can i calculate nmol?

2-Is nmol=mol water+mol cnt+mol protein?

Thanks in advance
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[gmx-users] interaction energy

[maryam haji]

Dear gromacs users

My system contains protein and CNT and water molecules.

I want to obtain interaction energy. There is following equation in some
papers:

E(int) = E(cnt+protein) - E(cnt) - E(protein).

Based on this equation, should 3 MD simulations?

1-  cnt in water

2- protein in water

3- protein and cnt in water

I have 3 questions:

1) Is my opinion true?

2) What means of E(x)? Are E(cnt) and E(protein) corresponded to total or
potential energy
of cnt and protein in simulation # 1 and 2?

3) Is E(cnt+protein) corresponded to total potential energy
of cnt+protein in simulation #  3 ?


Thanks in advance
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[gmx-users] Interaction energy of system as a function of the interface area

[maryam haji]

Dear all

My system consists of protein and CNT. I know I can calculate
Interaction energy and interface area using g_energy and g_sas tools,
respectively.

I want to obtain Interaction energy of my system as a function of the
interface area between the protein and CNT.

How to do this?

Any help will highly appreciated.
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[gmx-users] protein-cnt

[maryam haji]

I am doing simulation of the protein-cnt complex.How can I compute the
protein-SWCNT interface area and interaction energy and heat capacity for
cnt?

Thank you
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