Re: [gmx-users] Geometry Optimization for Metal organic Frame works

2018-03-07 Thread Smith, Micholas D. 
I would contact the OBGMX folks concerning this, as it sound like a software 
issue. If it works to produce a topology file for your initial coordinate 
system but not your optimized coordinates (presuming the same system 
composition, just modified geometry) than something seems amiss with their 
webserver.

Regards,

Micholas

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Nagasree 
Garapati <nagasree.garap...@mail.wvu.edu>
Sent: Wednesday, March 07, 2018 8:25 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Fw: Geometry Optimization for Metal organic Frame works

Thank You Micholas


I have created the topology files using initial input file in OBGMX and it 
shows that there are 20 unique bond terms, out of which there are 3 bonds 
between the metal ion and the N2 in linker.

However, when I tried to create topolgies using the optimized final output 
(final.gro) file in OBGMX, nothing is created I have empty files for both .top 
and .itp files.

I believe there is something wrong with the topology files, but I am not able 
to figure out where is the mistake.

Any suggestions ?


Thank You


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028<tel:304%20293-5028>(O)
304 276-3674(M)

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Re: [gmx-users] Geometry Optimization for Metal organic Frame works

2018-03-06 Thread Smith, Micholas D. 
Alternatively, if the visualization is the only place you don't see the bond 
(but if you check the topology file and it does show a bond between the metal 
and the linker is defined) it could be a visualization issue. In that case look 
at the trjconv command options to center the system and account for the pbc's.

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: Smith, Micholas D.
Sent: Tuesday, March 06, 2018 10:52 AM
To: gmx-us...@gromacs.org
Subject: Re: Geometry Optimization for Metal organic Frame works

Its the topology generation. It didn't capture that a bond should be where you 
expected it to be. Bonds will not break in gromacs, so if you are seeing less 
bonds than you expected its in the topology.


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Nagasree 
Garapati <nagasree.garap...@mail.wvu.edu>
Sent: Tuesday, March 06, 2018 10:49 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Geometry Optimization for Metal organic Frame works

Hi All


I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic 
Data Center (CCDC) and used OBGMX tool to develop force field parameters and 
used following minim.mdp file for optimization. But after optimization, when I 
visualize the output .gro file I see that all the bonds between the Metal atom 
and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp 
file. If anyone has experience with modeling MOFs using GROMACS, I really 
appreciate your help.


Thank You


; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 2.0 ; Short-range electrostatic cut-off
rvdw = 2.0 ; Short-range Van der Waals cut-off
rlist = 2.0 ; Short-range neighbor cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028<tel:304%20293-5028>(O)
304 276-3674(M)

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Re: [gmx-users] Geometry Optimization for Metal organic Frame works

2018-03-06 Thread Smith, Micholas D. 
Its the topology generation. It didn't capture that a bond should be where you 
expected it to be. Bonds will not break in gromacs, so if you are seeing less 
bonds than you expected its in the topology.


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Nagasree 
Garapati <nagasree.garap...@mail.wvu.edu>
Sent: Tuesday, March 06, 2018 10:49 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Geometry Optimization for Metal organic Frame works

Hi All


I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic 
Data Center (CCDC) and used OBGMX tool to develop force field parameters and 
used following minim.mdp file for optimization. But after optimization, when I 
visualize the output .gro file I see that all the bonds between the Metal atom 
and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp 
file. If anyone has experience with modeling MOFs using GROMACS, I really 
appreciate your help.


Thank You


; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 2.0 ; Short-range electrostatic cut-off
rvdw = 2.0 ; Short-range Van der Waals cut-off
rlist = 2.0 ; Short-range neighbor cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028<tel:304%20293-5028>(O)
304 276-3674(M)

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[gmx-users] Geometry Optimization for Metal organic Frame works

2018-03-06 Thread Nagasree Garapati 

Hi All


I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic 
Data Center (CCDC) and used OBGMX tool to develop force field parameters and 
used following minim.mdp file for optimization. But after optimization, when I 
visualize the output .gro file I see that all the bonds between the Metal atom 
and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp 
file. If anyone has experience with modeling MOFs using GROMACS, I really 
appreciate your help.


Thank You


; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 2.0 ; Short-range electrostatic cut-off
rvdw = 2.0 ; Short-range Van der Waals cut-off
rlist = 2.0 ; Short-range neighbor cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028(O)
304 276-3674(M)

-- 
Gromacs Users mailing list

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