[gmx-users] GPU offload for reaction-field type dataset

[Jimmy Chen]

Hi,

there's only rf(reaction-field) dataset in

https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseB.tar.gz


Per user guide (getting  good performance from mdrun),

Native GPU acceleration is supported with the Verlet cut-off scheme

(not
with the group scheme) with PME, reaction-field, and plain cut-off
electrostatics.

How to enable GPU offload for reaction-field type dataset?
I only can run gpu-offload for PP with it now, is there other way to enable
more GPU offload with this kind of dataset?
I'm using Nvidia V100 now.

btw, is interpolation orders other than 4 not supported for gpu-offload as
well?

Thanks,
Jimmy
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[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Mijiddorj B]

Dear Gmx users,

Currently, I am trying to assign the atomtypes in charmm27 for the
polyethyleneimine polymer. It includes several different groups of atoms. I
included following illustration and asignment:
##
 H CH2
 | /
NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...

##
I assigned and the charmm27 atomtypes as following and compared charmm36
atomtypes generated by CgenFF.
Atom   Charmm27 Charmm36
N (NH2) ---> NH2   |NG321
N (NH1) ---> NH1   |NG311
C (CH2) ---> CT2   |CG321
H (HC2) ---> HA |HGA2
N ?   |NG301

If you have any experience, please check my assignments the charmm27 atom
types and advice me the atomtype of the last Nitrogen, which were assigned
as NG301 with CgenFF.


Best Regards,

Mijiddorj
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Re: [gmx-users] GMXLIB for pdb2gmx

[Justin Lemkul]

On 11/19/19 6:55 PM, Ling Chan wrote:

Hello colleagues,

I would like to do experiments on a force field. Hence I cloned the force field 
files from shares/gromacs/top to a local directory, at $HOME/top. According to 
the manual page at 
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html
I need to set the GMXLIB environment variable to point to my directory. So I 
did. But then pdb2gmx still goes to the original directory, at 
shares/gromacs/top, before visiting $GMXLIB. As a result, the force fields are 
all duplicated and pdb2gmx would refuse to go ahead. This is probably the same 
issue as discussed here. https://redmine.gromacs.org/issues/1928

So, how can I prevent Gromacs from searching the original force field directory?


As described in that Redmine issue, you cannot override $GMXLIB, you can 
only append to it. If you wish to use modified versions of different 
force fields, you should copy that force field directory into the 
working directory and rename it, e.g. amber99.ff becomes amber99_mod.ff, 
etc.



On a related note, if I am to add new residues, say Glycam ones, I would need 
to append new lines to the file “residuetypes.dat”, at share/gromacs/top. If I 
have a “residuetypes.dat” both at share/gromacs/top and at $GMXLIB, will 
pdb2gmx read both files?


Only one file is read. pdb2gmx will look in the working directory first, 
then $GMXLIB, and will use the first one that it finds.


-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] GMXLIB for pdb2gmx

[Ling Chan]

Hello colleagues,

I would like to do experiments on a force field. Hence I cloned the force field 
files from shares/gromacs/top to a local directory, at $HOME/top. According to 
the manual page at 
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html
I need to set the GMXLIB environment variable to point to my directory. So I 
did. But then pdb2gmx still goes to the original directory, at 
shares/gromacs/top, before visiting $GMXLIB. As a result, the force fields are 
all duplicated and pdb2gmx would refuse to go ahead. This is probably the same 
issue as discussed here. https://redmine.gromacs.org/issues/1928

So, how can I prevent Gromacs from searching the original force field directory?

On a related note, if I am to add new residues, say Glycam ones, I would need 
to append new lines to the file “residuetypes.dat”, at share/gromacs/top. If I 
have a “residuetypes.dat” both at share/gromacs/top and at $GMXLIB, will 
pdb2gmx read both files?

Thank you.

Regards,
Ling

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Re: [gmx-users] protein_ligand error NVT

[Bratin Kumar Das]

You can minimise the system in vaccum. If it is not running properly there
might be some problem in topology. If it is running proper ...you have to
delete water molecule from the surface of the protein...and then minimize.

On Tue 19 Nov, 2019, 9:32 PM Justin Lemkul,  wrote:

>
>
> On 11/19/19 10:30 PM, Iman Katouzian wrote:
> > Good day.
> >
> > I have encountered a problem in my protein-ligand simulation as after the
> > energy minimization step, when I run the gmx mdrun -deffnm nvt
> > I encounter the error segmentation faiulire core dumped :
> >
> > step 1: One or more water molecules can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> >
> > Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8#
> >
> > Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8#
> > Wrote pdb files with previous and current coordinates
> > *Segmentation fault (core dumped)*
>
>
> http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system
>
> -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] protein_ligand error NVT

[Justin Lemkul]

On 11/19/19 10:30 PM, Iman Katouzian wrote:

Good day.

I have encountered a problem in my protein-ligand simulation as after the
energy minimization step, when I run the gmx mdrun -deffnm nvt
I encounter the error segmentation faiulire core dumped :

step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8#
Wrote pdb files with previous and current coordinates
*Segmentation fault (core dumped)*


http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system

-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] protein_ligand error NVT

[Iman Katouzian]

Good day.

I have encountered a problem in my protein-ligand simulation as after the
energy minimization step, when I run the gmx mdrun -deffnm nvt
I encounter the error segmentation faiulire core dumped :

step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8#
Wrote pdb files with previous and current coordinates
*Segmentation fault (core dumped)*

Thanks.

-- 

*Iman Katouzian*

*Ph.D.** candidate of Food Process Engineering*

*Faculty of Food Science and Technology*

*University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 11/19/19 5:55 AM, Bratin Kumar Das wrote:

Hi
 I hope there is a problem in the topology...please follow the gromacs
tutorial..


More specifically: http://www.mdtutorials.com/gmx/complex/index.html

The #include statements are out of order. You cannot add new parameters 
to the topology after any [moleculetype] has been declared. The entire 
force field must be known before any species can be introduced.


-Justin


On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:


Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:


Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to

the

system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
  ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand parameters
#include "lig.prm"

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"

I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file

for

reference.



Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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==

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] Fatal error during mdrun

[Samayaditya Singh]

Hi ,I am having an error during running the mdrun for  homo-dimer of a 
protein-ligand complex of Ribokinase on server, I used Charmm36 FF parameters 
for both ligands and protein. can u please give some advice.
Changing nstlist from 10 to 20, rlist from 1 to 1.028
Input Parameters:   integrator                     = md   tinit                 
         = 0   dt                             = 0.002   nsteps                  
       = 1000   init-step                      = 0   simulation-part        
        = 1   comm-mode                      = Linear   nstcomm                 
       = 100   bd-fric                        = 0   ld-seed                     
   = 1535035550   emtol                          = 10   emstep                  
       = 0.01   niter                          = 20   fcstep                    
     = 0   nstcgsteep                     = 1000   nbfgscorr                    
  = 10   rtpi                           = 0.05   nstxout                        
= 5000   nstvout                        = 5000   nstfout                        
= 0   nstlog                         = 5000   nstcalcenergy                  = 
100   nstenergy                      = 5000   nstxout-compressed             = 
5000   compressed-x-precision         = 5000   cutoff-scheme                  = 
Verlet   nstlist                        = 20   ns-type                        = 
Grid   pbc                            = xyz   periodic-molecules             = 
FALSE   verlet-buffer-tolerance        = 0.005   rlist                          
= 1.028   rlistlong                      = 1.028   nstcalclr                    
  = 10   coulombtype                    = PME   coulomb-modifier               
= Potential-shift   rcoulomb-switch                = 0   rcoulomb               
        = 1   epsilon-r                      = 1   epsilon-rf                   
  = inf   vdw-type                       = Cut-off   vdw-modifier               
    = Potential-shift   rvdw-switch                    = 0   rvdw               
            = 1   DispCorr                       = EnerPres   table-extension   
             = 1   fourierspacing                 = 0.16   fourier-nx           
          = 72   fourier-ny                     = 72   fourier-nz               
      = 72   pme-order                      = 4   ewald-rtol                    
 = 1e-05   ewald-rtol-lj                  = 0.001   lj-pme-comb-rule            
   = Geometric   ewald-geometry                 = 0   epsilon-surface           
     = 0   implicit-solvent               = No   gb-algorithm                   
= Still   nstgbradii                     = 1   rgbradii                       = 
1   gb-epsilon-solvent             = 80   gb-saltconc                    = 0   
gb-obc-alpha                   = 1   gb-obc-beta                    = 0.8   
gb-obc-gamma                   = 4.85   gb-dielectric-offset           = 0.009  
 sa-algorithm                   = Ace-approximation   sa-surface-tension        
     = 2.05016   tcoupl                         = V-rescale   nsttcouple        
             = 10   nh-chain-length                = 0   
print-nose-hoover-chain-variables = FALSE   pcoupl                         = 
Parrinello-Rahman   pcoupltype                     = Isotropic   nstpcouple     
                = 10   tau-p                          = 2   compressibility 
(3x3):      compressibility[    0]={ 4.5e-05,  0.0e+00,  0.0e+00}   
   compressibility[    1]={ 0.0e+00,  4.5e-05,  0.0e+00}      
compressibility[    2]={ 0.0e+00,  0.0e+00,  4.5e-05}   ref-p 
(3x3):      ref-p[    0]={ 1.0e+00,  0.0e+00,  0.0e+00}      ref-p[ 
   1]={ 0.0e+00,  1.0e+00,  0.0e+00}      ref-p[    2]={ 
0.0e+00,  0.0e+00,  1.0e+00}   refcoord-scaling               = No  
 posres-com (3):      posres-com[0]= 0.0e+00      posres-com[1]= 
0.0e+00      posres-com[2]= 0.0e+00   posres-comB (3):      
posres-comB[0]= 0.0e+00      posres-comB[1]= 0.0e+00      
posres-comB[2]= 0.0e+00   QMMM                           = FALSE   
QMconstraints                  = 0   QMMMscheme                     = 0   
MMChargeScaleFactor            = 1qm-opts:   ngQM                           = 0 
  constraint-algorithm           = Lincs   continuation                   = 
TRUE   Shake-SOR                      = FALSE   shake-tol                      
= 0.0001   lincs-order                    = 4   lincs-iter                     
= 1   lincs-warnangle                = 30   nwall                          = 0  
 wall-type                      = 9-3   wall-r-linpot                  = -1   
wall-atomtype[0]               = -1   wall-atomtype[1]               = -1   
wall-density[0]                = 0   wall-density[1]                = 0   
wall-ewald-zfac                = 3   pull                           = FALSE   
rotation                       = FALSE   interactiveMD                  = FALSE 
  disre

Re: [gmx-users] eelctric field

[Amin Rouy]

Dear  Christian,

Thank  you, I appreciate your help.

On Tue, Nov 19, 2019 at 11:59 AM Christian Blau  wrote:

> Hi Amin,
>
>
> Sorry for the late answer - when calculating the pressure, no information
> about the electric field is used (as it should
> be). To obtain the pressure as if no electric field were applied, running
> another simulation with the field switched off
> is the only way.
>
>
> Best,
>
> Christian
>
> On 11/15/19 3:20 PM, Amin Rouy wrote:
> > Dear Christian,
> >
> > Thank you for the answer.  My last question I hope:
> >
> > I just noticed that the pressure I get in y and z directions seem
> physical
> > and correct, but the x direction of pressure is a big negative number and
> > not reasonable (Pres-ZZ = -400 bar). (I had applied the filed in x
> > direction and I have NVT ensemble). So I think the way Gromacs calculates
> > the pressure in presence applied field does not take into account the
> field
> > effect, am I correct?
> >
> > On Fri, Nov 15, 2019 at 11:17 AM Christian Blau  wrote:
> >
> >> Hello Amin,
> >>
> >>
> >> Though the forces are present during the simulation the additional work
> on
> >> the system that is exerted via the electric
> >> field is not output as an additional energy term in GROMACS.
> >>
> >> I believe the pressure deviations that you observe are due to two
> >> different effects:
> >>
> >>   - the pressure fluctuates much more than energies, like coulomb
> >> interactions, etc., especially in small systems.
> >> The question here would be if the deviation between the perturbed and
> >> unperturbed system that you observe is larger than
> >> the deviation between two unperturbed systems
> >>
> >>   - the electric field indirectly influences the pressure. I would
> >> expect this effect to be usually small, but if you
> >> imagine a system consisting only of the same number of positively and
> >> negatively charged ions, applying the electric
> >> field along z-direction will cause half of them to move upwards and the
> >> other half downwards along the z-direction,
> >> which will in turn affect the pressure.
> >>
> >>
> >> Best,
> >>
> >> Christian
> >>
> >> On 11/13/19 3:39 PM, Amin Rouy wrote:
> >>> Dear Christian,
> >>>
> >>> Thank you for your reply. However, still it is not fully clear to me.
> >> Lets
> >>> only talk about gmx energy.  How it happens that I get from gmx energy
> >>> similar values of energies (LJ, columbs, total energies) while a
> >> different
> >>> pressure, with and without applied filed? The total energy should be
> >>> different as a result of an additional energy due to applied filed on
> >> each
> >>> atom.
> >>>
> >>> On Wed, Nov 13, 2019 at 3:10 PM Christian Blau  wrote:
> >>>
>  Hello Amin,
> 
> 
>  When you apply an electric field during the simulation by setting the
> >> mdp
>  parameters like E-x =... as you describe,
>  nothing more happens than that each atom experiences an additional
> force
>  that is "atom charge * field strength". The
>  energy terms or virial (that then would relate to pressure coupling)
> are
>  not influenced by this. If these terms differ
>  between a simulation with electric field and one without, then only
>  because the system as a whole responds to the
>  applied electric field.
> 
>  gmx potential on the other hand is an analysis tool that is per se
>  unrelated on how you chose to apply an electric field
>  during your simulation or not. However, when applying an electric
> field,
>  you would expect a different result from an
>  analysis with gmx potential than without electric field, because your
>  system will respond to the applied electric field.
> 
> 
>  Best,
> 
>  Christian
> 
>  On 11/13/19 2:44 PM, Amin Rouy wrote:
> > Hi,
> >
> > I am using gromacs 5.0.4. I apply a uniform electric field in x
> >> direction
> > of my box (no walls),
> > E-x= 1  10  0, and simulation runs without error.
> > I notice that the values of electrostatic interactions I get from the
> > simulation is the same as without the an electric field. Which is
>  strange,
> > but according to previous questions in the gromacs forum this is
> true:
> > ''gmx potential only calculates the electric field and potential of
> the
> > system. It does not take into account the applied field.''
> >
> > Now, my question is are the other quantities obtaining from gmx
> energy
>  take
> > into account field effect? e.g. pressure of the system.
>  --
>  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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Re: [gmx-users] droplet

[Christian Blau]

Hi Alex,


I'm not sure this is really something for the GROMACS mailing list and I'm guessing the question you were asking - What 
is the expected behaviour of the solvent accessible surface area of a droplet with temperature?


Here is a "back-of-the envelope" estimate: The easiest model of a droplet is an effective harmonic potential that keeps 
together a bunch of molecules at the center of the coordinate system. A molecule at x has then the effective potential 
energy (chemical potential) E(x) = k * x^2, yielding a Boltzmann distribution of particle positions at a given 
temperature proportional to exp(-(kx^2)/(k_b T)). The droplet boundary is an iso-contour of this distribution - 
proportional to 1/T - the surface area is thus proportional to (1/T)^2. In an equilibrium situation you would expect 
your droplet SASA to go with T^(-2). Because quenching includes non-equilibrium effects, you might observe an exponent > -2.



Best,

Christian

On 11/18/19 10:28 PM, Alex wrote:

Dear all,
The surface area (calculated by gmx sasa) of a droplet of a molecule,
reduces during temperature quenching, I wonder if anybody has an idea to
explain that by calculation a meaningful quantity of the droplet?

Thank you
Alex

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Re: [gmx-users] eelctric field

[Christian Blau]

Hi Amin,


Sorry for the late answer - when calculating the pressure, no information about the electric field is used (as it should 
be). To obtain the pressure as if no electric field were applied, running another simulation with the field switched off 
is the only way.



Best,

Christian

On 11/15/19 3:20 PM, Amin Rouy wrote:

Dear Christian,

Thank you for the answer.  My last question I hope:

I just noticed that the pressure I get in y and z directions seem physical
and correct, but the x direction of pressure is a big negative number and
not reasonable (Pres-ZZ = -400 bar). (I had applied the filed in x
direction and I have NVT ensemble). So I think the way Gromacs calculates
the pressure in presence applied field does not take into account the field
effect, am I correct?

On Fri, Nov 15, 2019 at 11:17 AM Christian Blau  wrote:


Hello Amin,


Though the forces are present during the simulation the additional work on
the system that is exerted via the electric
field is not output as an additional energy term in GROMACS.

I believe the pressure deviations that you observe are due to two
different effects:

  - the pressure fluctuates much more than energies, like coulomb
interactions, etc., especially in small systems.
The question here would be if the deviation between the perturbed and
unperturbed system that you observe is larger than
the deviation between two unperturbed systems

  - the electric field indirectly influences the pressure. I would
expect this effect to be usually small, but if you
imagine a system consisting only of the same number of positively and
negatively charged ions, applying the electric
field along z-direction will cause half of them to move upwards and the
other half downwards along the z-direction,
which will in turn affect the pressure.


Best,

Christian

On 11/13/19 3:39 PM, Amin Rouy wrote:

Dear Christian,

Thank you for your reply. However, still it is not fully clear to me.

Lets

only talk about gmx energy.  How it happens that I get from gmx energy
similar values of energies (LJ, columbs, total energies) while a

different

pressure, with and without applied filed? The total energy should be
different as a result of an additional energy due to applied filed on

each

atom.

On Wed, Nov 13, 2019 at 3:10 PM Christian Blau  wrote:


Hello Amin,


When you apply an electric field during the simulation by setting the

mdp

parameters like E-x =... as you describe,
nothing more happens than that each atom experiences an additional force
that is "atom charge * field strength". The
energy terms or virial (that then would relate to pressure coupling) are
not influenced by this. If these terms differ
between a simulation with electric field and one without, then only
because the system as a whole responds to the
applied electric field.

gmx potential on the other hand is an analysis tool that is per se
unrelated on how you chose to apply an electric field
during your simulation or not. However, when applying an electric field,
you would expect a different result from an
analysis with gmx potential than without electric field, because your
system will respond to the applied electric field.


Best,

Christian

On 11/13/19 2:44 PM, Amin Rouy wrote:

Hi,

I am using gromacs 5.0.4. I apply a uniform electric field in x

direction

of my box (no walls),
E-x= 1  10  0, and simulation runs without error.
I notice that the values of electrostatic interactions I get from the
simulation is the same as without the an electric field. Which is

strange,

but according to previous questions in the gromacs forum this is true:
''gmx potential only calculates the electric field and potential of the
system. It does not take into account the applied field.''

Now, my question is are the other quantities obtaining from gmx energy

take

into account field effect? e.g. pressure of the system.

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Re: [gmx-users] (no subject)

[Bratin Kumar Das]

Hi
I hope there is a problem in the topology...please follow the gromacs
tutorial..

On Tue 19 Nov, 2019, 3:34 PM Alessandra Villa, <
alessandra.villa.bio...@gmail.com> wrote:

> Hi,
> Pls note that the maillist does not support attachments.
> Also it will better/helpful to use emails subject.
> Kind regards
> Alessandra
>
> On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
> wrote:
>
> > Dear All,
> > I am doing a protein-ligand simulation, when i was try to *add ions to
> the
> > system*
> > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> > *there was an error*
> > Fatal error:
> > Syntax error - File lig.prm, line 2
> > Last line read:
> > '[ bondtypes ]'
> > Invalid order for directive bondtypes
> > *my topol.top- ligand defination is as follows *
> >  ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include ligand parameters
> > #include "lig.prm"
> >
> > ; Include ligand topology
> > #include "lig.itp"
> >
> > ; Include water topology
> > #include "./charmm36-mar2019.ff/tip3p.itp"
> >
> > I have included the ligand parameter details as suggested in lig.top file
> > generated by cgenff python script. I have attached the itp and prm file
> for
> > reference.
> >
> >
> >
> > Thanks & Regards,
> > Dr. Pooja Kesari
> > Post Doctoral Fellow
> > Department Of Biosciences and Bioengineering
> > Indian Institute of Technology Bombay
> > INDIA
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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Re: [gmx-users] Regarding LSI calculation

[Christian Blau]

Hi Omar,


Though I don't know of any GROMACS tool that can calculate the local structure 
index, some third-party tool might help, like

https://pypi.org/project/iOrder/


The input file format for above tool is .xyz which you can obtain from a 
GROMACS trajectory using the MDAnalysis tools here:

https://www.mdanalysis.org/docs/documentation_pages/coordinates/XYZ.html#xyz-format


Best,

Christian

On 11/11/19 4:40 AM, Omkar Singh wrote:

Hi everyone,
  I want to find out LSI (local structural Index) for my protein water
system. Can anybody help me regarding this issue?

Thank you

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Re: [gmx-users] How to prepare protein-peptide/protein-ligand complex molecule in membrane environment

[Bratin Kumar Das]

Hi
You can see the gromacs tutorial by Dr. Lemkul
Otherwise you can go for CHARMM gui

The following tutorial may help you
https://youtu.be/VNytjlJ1r6s

On Tue 19 Nov, 2019, 2:29 PM Muthusankar,  wrote:

> Dear All,
> Currently am working in integral membrane protein and i have docked complex
> molecule of protein-peptide/protein-ligand. i am planning to run the MD
> simulation using gromacs. I need to prepare the membrane environment of
> complex molecules. Please, guide me, how to prepare the
> protein-peptide/protein-ligand complex molecule in membrane environment?
>
> Thanks.
>
> With regards
> *Muthu Sankar*
> Biomedical Informatics Centre,
> ICMR-National Institute for Research in Reproductive Health (NIRRH),
> Parel, Mumbai-400 012, India.
>
> Email: muthubio...@gmail.com; muthubio...@gmail.com
> Mobile No.  +91 9080444540; 9789765123
> --
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> posting!
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>
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>
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Re: [gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics)

[Christian Blau]

Hi Xavier,


Bugs are usually best reported via "redmine.gromacs.org". You can self-report when registering there. In this case I 
just went ahead and filed the bug report, if you want to add information to the bug report and check how things are 
developing you can check here:


https://redmine.gromacs.org/issues/3209

There, you can also attach files to the bug report. The most helpful thing for fixing a GROMACS bug is a complete set of 
input files (at least the .tpr though) that reliably reproduces the bug. (Ideally the tiniest system you can conceive, 
but any system is much much better than none)



The video that you linked is also extremely nice to have and helpful

Thanks for the report!

Best,

Christian


On 11/19/19 11:11 AM, Xavier Martinez wrote:

Dear gmx users,

I came across a bug that is reproducible when using the IMD implementation in several versions of Gromacs including 
2019.3 and different operating systems.


This bug occurs with the following steps:

- Run an IMD simulation (gmx mdrun -imdwait -imdpull -imdterm -s mysim.tpr)

- Connect to the simulation using VMD (or other visualization tool that 
implements the IMD protocol)

- Pause the simulation from VMD ("detach sim" button)

- Reconnect to the simulation

The expected behavior is to have the same performance before and after pausing 
the simulation.

The actual behavior is a slower and stuttering simulation. Note that this bug 
does not occur when using NAMD.

See an example of the bug here: https://www.youtube.com/watch?v=_gZ6wA7c4b8 



An error line appears in the gromacs window: "IMD: Failed to shutdown socket. Did the client already disconnect?" and 
"IMD: Error in file gromacs-2019.3/src/gromacs/imd/imdsocket.cpp on line 293."


How should I proceed to help this bug getting fixed ?

Best regards,

Xavier Martinez, Ph.D

CNRS-IBPC LBT, Paris



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[gmx-users] Potential bug in IMD implementation (Interactive Molecular Dynamics)

[Xavier Martinez]

Dear gmx users,

I came across a bug that is reproducible when using the IMD 
implementation in several versions of Gromacs including 2019.3 and 
different operating systems.


This bug occurs with the following steps:

- Run an IMD simulation (gmx mdrun -imdwait -imdpull -imdterm -s mysim.tpr)

- Connect to the simulation using VMD (or other visualization tool that 
implements the IMD protocol)


- Pause the simulation from VMD ("detach sim" button)

- Reconnect to the simulation

The expected behavior is to have the same performance before and after 
pausing the simulation.


The actual behavior is a slower and stuttering simulation. Note that 
this bug does not occur when using NAMD.


See an example of the bug here: 
https://www.youtube.com/watch?v=_gZ6wA7c4b8 



An error line appears in the gromacs window: "IMD: Failed to shutdown 
socket. Did the client already disconnect?" and "IMD: Error in file 
gromacs-2019.3/src/gromacs/imd/imdsocket.cpp on line 293."


How should I proceed to help this bug getting fixed ?

Best regards,

Xavier Martinez, Ph.D

CNRS-IBPC LBT, Paris


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Re: [gmx-users] (no subject)

[Alessandra Villa]

Hi,
Pls note that the maillist does not support attachments.
Also it will better/helpful to use emails subject.
Kind regards
Alessandra

On Tue, Nov 19, 2019 at 10:46 AM pooja kesari 
wrote:

> Dear All,
> I am doing a protein-ligand simulation, when i was try to *add ions to the
> system*
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> *there was an error*
> Fatal error:
> Syntax error - File lig.prm, line 2
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
> *my topol.top- ligand defination is as follows *
>  ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand parameters
> #include "lig.prm"
>
> ; Include ligand topology
> #include "lig.itp"
>
> ; Include water topology
> #include "./charmm36-mar2019.ff/tip3p.itp"
>
> I have included the ligand parameter details as suggested in lig.top file
> generated by cgenff python script. I have attached the itp and prm file for
> reference.
>
>
>
> Thanks & Regards,
> Dr. Pooja Kesari
> Post Doctoral Fellow
> Department Of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> INDIA
> --
> 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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[gmx-users] (no subject)

[pooja kesari]

Dear All,
I am doing a protein-ligand simulation, when i was try to *add ions to the
system*
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
*there was an error*
Fatal error:
Syntax error - File lig.prm, line 2
Last line read:
'[ bondtypes ]'
Invalid order for directive bondtypes
*my topol.top- ligand defination is as follows *
 ; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ligand parameters
#include "lig.prm"

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "./charmm36-mar2019.ff/tip3p.itp"

I have included the ligand parameter details as suggested in lig.top file
generated by cgenff python script. I have attached the itp and prm file for
reference.



Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
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[gmx-users] How to prepare protein-peptide/protein-ligand complex molecule in membrane environment

[Muthusankar]

Dear All,
Currently am working in integral membrane protein and i have docked complex
molecule of protein-peptide/protein-ligand. i am planning to run the MD
simulation using gromacs. I need to prepare the membrane environment of
complex molecules. Please, guide me, how to prepare the
protein-peptide/protein-ligand complex molecule in membrane environment?

Thanks.

With regards
*Muthu Sankar*
Biomedical Informatics Centre,
ICMR-National Institute for Research in Reproductive Health (NIRRH),
Parel, Mumbai-400 012, India.

Email: muthubio...@gmail.com; muthubio...@gmail.com
Mobile No.  +91 9080444540; 9789765123
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