date:20171119

Re: [gmx-users] mdrun GPU

2017-11-19 Thread Mark Abraham

Hi,

For NVIDIA GPUs you should use their drivers and a CUDA build. It looks
like you are using other drivers and an OpenCL build, which is completely
untested.

Mark

On Mon, 20 Nov 2017 06:51 Ragothaman Yennamalli 
wrote:

> Hi,
> I have been reading this (
>
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> )
> and trying to run mdrun in a GPU based system. Unfortunately, I don't
> understand what the error is and how to troubleshoot it. Copy pasted below
> is the output I got for gmx mdrun.
>
> I tried assigning the GPU ids using the examples provided in the link above
> but have been unsuccessful. Please help me in troubleshooting this.
>
> Thanks and Regards,
> Raghu
>
> [student@localhost test]$ gmx mdrun -v -deffnm em
>   :-) GROMACS - gmx mdrun, 2016.4 (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> Karkoulis
> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
>Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
>   Teemu Virolainen  Christian WennbergMaarten Wolf
>and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2017, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS:  gmx mdrun, version 2016.4
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /home/student/test
> Command line:
>   gmx mdrun -v -deffnm em
>
>
> Back Off! I just backed up em.log to ./#em.log.6#
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> cl_get_gt_device(): error, unknown device: 0
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> cl_get_gt_device(): error, unknown device: 0
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or incorrect rendering.
> get chip id failed: -1 [22]
> param: 4, val: 0
> cl_get_gt_device(): error, unknown device: 0
> X server found. dri2 connection failed!
> DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
> Assuming 131072kB available aperture size.
> May lead to reduced performance or

Re: [gmx-users] Energy analysis

2017-11-19 Thread Amir Zeb

Yes Dr. Dallas,

I have gone through free energy analysis tutorial, But I'm wondering that
whether this tutorial is working for large molecule like protein or not?
Because the tutorial has explained methane only.
Your feedback will highly be appreciated.

Thanks!

Amir

On Sun, Nov 19, 2017 at 5:54 PM, Dallas Warren 
wrote:

> Always a good starting point 
>
> http://www.gromacs.org/Documentation/Tutorials
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 20 November 2017 at 12:34, Amir Zeb  wrote:
> > Thanks Mark,
> >
> > Depends what you mean by "stability."
> > Actually, I don't know the role of metal ion if it is used as co-factor
> by
> > a particular protein. I thought to do comparative analysis by MD
> simulation
> > which might predict the possible role of metal (in this case Zn^2+).
> Other
> > analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
> > already done, but I want to get insight in their energetic terms while
> > addressing the question why such changes occurred?
> > According to the best of my study, there is no experimental data
> available
> > for my target protein and that's why I want to predict its free-energy of
> > folding or whatever else.
> > Will you kindly suggest me some hand notes or tutorial like to do
> > free-energy analysis for both the systems; means a) protein with metal
> ion
> > and b) protein without metal ion?
> >
> > Amir
> >
> > On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> Depends what you mean by "stability." A well designed study could seek
> to
> >> measure or estimate the difference in the free-energy of folding, but
> that
> >> would probably require an infeasibly large amount of sampling, and be
> >> highly dependent on the quality of the parameterization of the
> >> metal-protein interactions, for which you would probably need some
> suitable
> >> experimental data.
> >>
> >> Mark
> >>
> >> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb  wrote:
> >>
> >> > Hi gromacs users,
> >> >
> >> > I want to calculate the energy for comparative analysis of protein
> with
> >> and
> >> > without metal ion, wherein I would like to determine the influence of
> >> metal
> >> > on protein structural stability. I have used gromacs for simulation.
> >> Please
> >> > suggest me how to do this kind of analysis? Should i follow a specific
> >> > tutorial?
> >> >
> >> > Amir
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at http://www.gromacs.org/
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>
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[gmx-users] mdrun GPU

2017-11-19 Thread Ragothaman Yennamalli

Hi,
I have been reading this (
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html)
and trying to run mdrun in a GPU based system. Unfortunately, I don't
understand what the error is and how to troubleshoot it. Copy pasted below
is the output I got for gmx mdrun.

I tried assigning the GPU ids using the examples provided in the link above
but have been unsuccessful. Please help me in troubleshooting this.

Thanks and Regards,
Raghu

[student@localhost test]$ gmx mdrun -v -deffnm em
  :-) GROMACS - gmx mdrun, 2016.4 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
  Teemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, version 2016.4
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /home/student/test
Command line:
  gmx mdrun -v -deffnm em


Back Off! I just backed up em.log to ./#em.log.6#
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
cl_get_gt_device(): error, unknown device: 0
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
cl_get_gt_device(): error, unknown device: 0
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
cl_get_gt_device(): error, unknown device: 0
X server found. dri2 connection failed!
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [22]
param: 4, val: 0
cl_get_gt_device(): error, unknown device: 0

Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU

Re: [gmx-users] Energy analysis

2017-11-19 Thread Dallas Warren

Always a good starting point 

http://www.gromacs.org/Documentation/Tutorials
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 20 November 2017 at 12:34, Amir Zeb  wrote:
> Thanks Mark,
>
> Depends what you mean by "stability."
> Actually, I don't know the role of metal ion if it is used as co-factor by
> a particular protein. I thought to do comparative analysis by MD simulation
> which might predict the possible role of metal (in this case Zn^2+). Other
> analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
> already done, but I want to get insight in their energetic terms while
> addressing the question why such changes occurred?
> According to the best of my study, there is no experimental data available
> for my target protein and that's why I want to predict its free-energy of
> folding or whatever else.
> Will you kindly suggest me some hand notes or tutorial like to do
> free-energy analysis for both the systems; means a) protein with metal ion
> and b) protein without metal ion?
>
> Amir
>
> On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Depends what you mean by "stability." A well designed study could seek to
>> measure or estimate the difference in the free-energy of folding, but that
>> would probably require an infeasibly large amount of sampling, and be
>> highly dependent on the quality of the parameterization of the
>> metal-protein interactions, for which you would probably need some suitable
>> experimental data.
>>
>> Mark
>>
>> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb  wrote:
>>
>> > Hi gromacs users,
>> >
>> > I want to calculate the energy for comparative analysis of protein with
>> and
>> > without metal ion, wherein I would like to determine the influence of
>> metal
>> > on protein structural stability. I have used gromacs for simulation.
>> Please
>> > suggest me how to do this kind of analysis? Should i follow a specific
>> > tutorial?
>> >
>> > Amir
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
-- 
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Re: [gmx-users] Energy analysis

2017-11-19 Thread Amir Zeb

Thanks Mark,

Depends what you mean by "stability."
Actually, I don't know the role of metal ion if it is used as co-factor by
a particular protein. I thought to do comparative analysis by MD simulation
which might predict the possible role of metal (in this case Zn^2+). Other
analysis like RMSD, RMSF, Rg, SASA, and structural analysis etc. I have
already done, but I want to get insight in their energetic terms while
addressing the question why such changes occurred?
According to the best of my study, there is no experimental data available
for my target protein and that's why I want to predict its free-energy of
folding or whatever else.
Will you kindly suggest me some hand notes or tutorial like to do
free-energy analysis for both the systems; means a) protein with metal ion
and b) protein without metal ion?

Amir

On Sun, Nov 19, 2017 at 11:32 AM, Mark Abraham 
wrote:

> Hi,
>
> Depends what you mean by "stability." A well designed study could seek to
> measure or estimate the difference in the free-energy of folding, but that
> would probably require an infeasibly large amount of sampling, and be
> highly dependent on the quality of the parameterization of the
> metal-protein interactions, for which you would probably need some suitable
> experimental data.
>
> Mark
>
> On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb  wrote:
>
> > Hi gromacs users,
> >
> > I want to calculate the energy for comparative analysis of protein with
> and
> > without metal ion, wherein I would like to determine the influence of
> metal
> > on protein structural stability. I have used gromacs for simulation.
> Please
> > suggest me how to do this kind of analysis? Should i follow a specific
> > tutorial?
> >
> > Amir
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham

Hi,

You can't decompose the "turning off" in the FE code by groups. You can
turn off the coulomb in the protein, but that turns off its interactions
with itself, solvent, and anything else

Mark

On Sun, Nov 19, 2017 at 9:27 PM Justin Lemkul  wrote:

>
>
> On 11/19/17 3:42 PM, Mark Abraham wrote:
> > Hi,
> >
> > Oh, I see. Yes that feature turns off both kinds of non-bonded
> > interactions. Then there is nothing useful for what you want.
>
> Couldn't this be done with the free energy code?
>
> Turn off protein-water electrostatics by running in the lambda=1 state
> with:
>
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw
> couple-intramol = no
>
> Then switch to couple-intramol = yes to turn off protein-protein
> interactions.
>
> I imagine it would be a huge memory hog and would run really slowly, but
> it's a possible solution.
>
> -Justin
>
> > Mark
> >
> > On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan 
> wrote:
> >
> >> Hi Mark,
> >>
> >> I apologize if I did not describe my problem correctly the first time,
> but
> >> I need the VdW interactions to stay on between all atoms at all times. I
> >> only need to turn off the electrostatic interactions between water and
> >> proteins.
> >>
> >> Thanks,
> >>
> >> Aram
> >>
> >> Hi,
> >>> You've described the feature correctly. Whether it is useful in a study
> >>> design is another matter :-)
> >>>
> >>> Mark
> >>>
> >>> On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan 
> >>> wrote:
> >>>
>  Hi Mark,
> 
>  I am not sure I understood. If I for example say "energygrp-excl =
> >>> Protein
>  Water" would not I turn off all the non-bonded interactions between
> >> water
>  and protein? Or did you mean something else?
> 
>  Thanks,
> 
>  Aram
> 
> 
> > Hi,
> >
> > In the group scheme you can turn on energy-group exclusions to get
> >> this
> > working, but of course all of those states are sampling unphysical
> >>> things
> > from a broken forcefield. That can be OK, but you will have to be
> >> able
> >>> to
> > defend that claim.
> >
> > Mark
> >
> > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan  > wrote:
> >
> >> Hello,
> >>
> >> I am running simulations of two protein domains in tip4p water and
>  0.15M
> >> salt concentration that contain up to 650,000 atoms total. The
> >>> protein
> >> domains are separated from each other at the start of each
> >> simulation
> > and I
> >> am measuring how the distance between them changes over time.
> >>
> >> Now, I need to do the same simulations, but with electrostatics
> >>> between
> >> proteins and water turned off (with water-water, protein-protein,
> >> ion-water, ion-protein electrostatics remaining). Then I need to
> >>> repeat
> >> that, but additionally turning off electrostatics between the two
> > domains.
> >> Water-water, ion-water, ion-protein, intra-domain electrostatics
> >>> should
> >> remain on.
> >>
> >> What will be the best way to do this?
> >>
> >> I am using CHARMM27 force field and the following settings to run
> >> the
> >> production simulations:
> >>
> >> integrator  = md
> >> dt  = 0.002
> >> nsteps  = 100 ; 2ns
> >> nstlog  = 1000
> >> nstxout = 5000
> >> nstvout = 5000
> >> nstfout = 5000
> >> nstcalcenergy   = 100
> >> nstenergy   = 1000
> >> ;
> >> cutoff-scheme   = Verlet
> >> nstlist = 20
> >> rlist   = 1.2
> >> coulombtype = pme
> >> rcoulomb= 1.2
> >> vdwtype = Cut-off
> >> vdw-modifier= Force-switch
> >> rvdw_switch = 1.0
> >> rvdw= 1.2
> >> ;
> >> tcoupl  = Nose-Hoover
> >> tc_grps = Protein Non-Protein
> >> tau_t   = 1.0 1.0
> >> ref_t   = 300.0   300.0
> >> ;
> >> pcoupl  = Parrinello-Rahman
> >> pcoupltype  = isotropic
> >> tau_p   = 5.0
> >> compressibility = 4.5e-5
> >> ref_p   = 1.0
> >> ;
> >> constraints = h-bonds
> >> constraint_algorithm= LINCS
> >> continuation= yes
> >> ;
> >> nstcomm = 100
> >> comm_mode   = linear
> >> comm_grps   = Protein Non-Protein
> >> ;
> >> refcoord_scaling= com
> >>
> >>
> >> I have tried to use the energy groups (energygrp-table) to specify
> >> interaction tables between water and protein, where I would set the
> >> electrostatic

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Justin Lemkul




On 11/19/17 3:42 PM, Mark Abraham wrote:

Hi,

Oh, I see. Yes that feature turns off both kinds of non-bonded
interactions. Then there is nothing useful for what you want.


Couldn't this be done with the free energy code?

Turn off protein-water electrostatics by running in the lambda=1 state with:

couple-lambda0 = vdw-q
couple-lambda1 = vdw
couple-intramol = no

Then switch to couple-intramol = yes to turn off protein-protein 
interactions.


I imagine it would be a huge memory hog and would run really slowly, but 
it's a possible solution.


-Justin


Mark

On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan  wrote:


Hi Mark,

I apologize if I did not describe my problem correctly the first time, but
I need the VdW interactions to stay on between all atoms at all times. I
only need to turn off the electrostatic interactions between water and
proteins.

Thanks,

Aram

Hi,

You've described the feature correctly. Whether it is useful in a study
design is another matter :-)

Mark

On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan 
wrote:


Hi Mark,

I am not sure I understood. If I for example say "energygrp-excl =

Protein

Water" would not I turn off all the non-bonded interactions between

water

and protein? Or did you mean something else?

Thanks,

Aram



Hi,

In the group scheme you can turn on energy-group exclusions to get

this

working, but of course all of those states are sampling unphysical

things

from a broken forcefield. That can be OK, but you will have to be

able

to

defend that claim.

Mark

On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham

Hi,

Oh, I see. Yes that feature turns off both kinds of non-bonded
interactions. Then there is nothing useful for what you want.

Mark

On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan  wrote:

> Hi Mark,
>
> I apologize if I did not describe my problem correctly the first time, but
> I need the VdW interactions to stay on between all atoms at all times. I
> only need to turn off the electrostatic interactions between water and
> proteins.
>
> Thanks,
>
> Aram
>
> Hi,
> >
> > You've described the feature correctly. Whether it is useful in a study
> > design is another matter :-)
> >
> > Mark
> >
> > On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan 
> > wrote:
> >
> > > Hi Mark,
> > >
> > > I am not sure I understood. If I for example say "energygrp-excl =
> > Protein
> > > Water" would not I turn off all the non-bonded interactions between
> water
> > > and protein? Or did you mean something else?
> > >
> > > Thanks,
> > >
> > > Aram
> > >
> > >
> > > > Hi,
> > > >
> > > > In the group scheme you can turn on energy-group exclusions to get
> this
> > > > working, but of course all of those states are sampling unphysical
> > things
> > > > from a broken forcefield. That can be OK, but you will have to be
> able
> > to
> > > > defend that claim.
> > > >
> > > > Mark
> > > >
> > > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan  >
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I am running simulations of two protein domains in tip4p water and
> > > 0.15M
> > > > > salt concentration that contain up to 650,000 atoms total. The
> > protein
> > > > > domains are separated from each other at the start of each
> simulation
> > > > and I
> > > > > am measuring how the distance between them changes over time.
> > > > >
> > > > > Now, I need to do the same simulations, but with electrostatics
> > between
> > > > > proteins and water turned off (with water-water, protein-protein,
> > > > > ion-water, ion-protein electrostatics remaining). Then I need to
> > repeat
> > > > > that, but additionally turning off electrostatics between the two
> > > > domains.
> > > > > Water-water, ion-water, ion-protein, intra-domain electrostatics
> > should
> > > > > remain on.
> > > > >
> > > > > What will be the best way to do this?
> > > > >
> > > > > I am using CHARMM27 force field and the following settings to run
> the
> > > > > production simulations:
> > > > >
> > > > > integrator  = md
> > > > > dt  = 0.002
> > > > > nsteps  = 100 ; 2ns
> > > > > nstlog  = 1000
> > > > > nstxout = 5000
> > > > > nstvout = 5000
> > > > > nstfout = 5000
> > > > > nstcalcenergy   = 100
> > > > > nstenergy   = 1000
> > > > > ;
> > > > > cutoff-scheme   = Verlet
> > > > > nstlist = 20
> > > > > rlist   = 1.2
> > > > > coulombtype = pme
> > > > > rcoulomb= 1.2
> > > > > vdwtype = Cut-off
> > > > > vdw-modifier= Force-switch
> > > > > rvdw_switch = 1.0
> > > > > rvdw= 1.2
> > > > > ;
> > > > > tcoupl  = Nose-Hoover
> > > > > tc_grps = Protein Non-Protein
> > > > > tau_t   = 1.0 1.0
> > > > > ref_t   = 300.0   300.0
> > > > > ;
> > > > > pcoupl  = Parrinello-Rahman
> > > > > pcoupltype  = isotropic
> > > > > tau_p   = 5.0
> > > > > compressibility = 4.5e-5
> > > > > ref_p   = 1.0
> > > > > ;
> > > > > constraints = h-bonds
> > > > > constraint_algorithm= LINCS
> > > > > continuation= yes
> > > > > ;
> > > > > nstcomm = 100
> > > > > comm_mode   = linear
> > > > > comm_grps   = Protein Non-Protein
> > > > > ;
> > > > > refcoord_scaling= com
> > > > >
> > > > >
> > > > > I have tried to use the energy groups (energygrp-table) to specify
> > > > > interaction tables between water and protein, where I would set the
> > > > > electrostatic potential to zero. However, given that
> energygrp-table
> > > and
> > > > > Varlet cutoff-scheme are incompatible, I could not make it work.
> But
> > it
> > > > is
> > > > > possible that I did something wrong.
> > > > >
> > > > > Thank you in advance,
> > > > >
> > > > > Aram
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > --
> > >

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Aram Davtyan

Hi Mark,

I apologize if I did not describe my problem correctly the first time, but
I need the VdW interactions to stay on between all atoms at all times. I
only need to turn off the electrostatic interactions between water and
proteins.

Thanks,

Aram

Hi,
>
> You've described the feature correctly. Whether it is useful in a study
> design is another matter :-)
>
> Mark
>
> On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan 
> wrote:
>
> > Hi Mark,
> >
> > I am not sure I understood. If I for example say "energygrp-excl =
> Protein
> > Water" would not I turn off all the non-bonded interactions between water
> > and protein? Or did you mean something else?
> >
> > Thanks,
> >
> > Aram
> >
> >
> > > Hi,
> > >
> > > In the group scheme you can turn on energy-group exclusions to get this
> > > working, but of course all of those states are sampling unphysical
> things
> > > from a broken forcefield. That can be OK, but you will have to be able
> to
> > > defend that claim.
> > >
> > > Mark
> > >
> > > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan 
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > I am running simulations of two protein domains in tip4p water and
> > 0.15M
> > > > salt concentration that contain up to 650,000 atoms total. The
> protein
> > > > domains are separated from each other at the start of each simulation
> > > and I
> > > > am measuring how the distance between them changes over time.
> > > >
> > > > Now, I need to do the same simulations, but with electrostatics
> between
> > > > proteins and water turned off (with water-water, protein-protein,
> > > > ion-water, ion-protein electrostatics remaining). Then I need to
> repeat
> > > > that, but additionally turning off electrostatics between the two
> > > domains.
> > > > Water-water, ion-water, ion-protein, intra-domain electrostatics
> should
> > > > remain on.
> > > >
> > > > What will be the best way to do this?
> > > >
> > > > I am using CHARMM27 force field and the following settings to run the
> > > > production simulations:
> > > >
> > > > integrator  = md
> > > > dt  = 0.002
> > > > nsteps  = 100 ; 2ns
> > > > nstlog  = 1000
> > > > nstxout = 5000
> > > > nstvout = 5000
> > > > nstfout = 5000
> > > > nstcalcenergy   = 100
> > > > nstenergy   = 1000
> > > > ;
> > > > cutoff-scheme   = Verlet
> > > > nstlist = 20
> > > > rlist   = 1.2
> > > > coulombtype = pme
> > > > rcoulomb= 1.2
> > > > vdwtype = Cut-off
> > > > vdw-modifier= Force-switch
> > > > rvdw_switch = 1.0
> > > > rvdw= 1.2
> > > > ;
> > > > tcoupl  = Nose-Hoover
> > > > tc_grps = Protein Non-Protein
> > > > tau_t   = 1.0 1.0
> > > > ref_t   = 300.0   300.0
> > > > ;
> > > > pcoupl  = Parrinello-Rahman
> > > > pcoupltype  = isotropic
> > > > tau_p   = 5.0
> > > > compressibility = 4.5e-5
> > > > ref_p   = 1.0
> > > > ;
> > > > constraints = h-bonds
> > > > constraint_algorithm= LINCS
> > > > continuation= yes
> > > > ;
> > > > nstcomm = 100
> > > > comm_mode   = linear
> > > > comm_grps   = Protein Non-Protein
> > > > ;
> > > > refcoord_scaling= com
> > > >
> > > >
> > > > I have tried to use the energy groups (energygrp-table) to specify
> > > > interaction tables between water and protein, where I would set the
> > > > electrostatic potential to zero. However, given that energygrp-table
> > and
> > > > Varlet cutoff-scheme are incompatible, I could not make it work. But
> it
> > > is
> > > > possible that I did something wrong.
> > > >
> > > > Thank you in advance,
> > > >
> > > > Aram
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> --
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham

Hi,

You've described the feature correctly. Whether it is useful in a study
design is another matter :-)

Mark

On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan  wrote:

> Hi Mark,
>
> I am not sure I understood. If I for example say "energygrp-excl = Protein
> Water" would not I turn off all the non-bonded interactions between water
> and protein? Or did you mean something else?
>
> Thanks,
>
> Aram
>
>
> > Hi,
> >
> > In the group scheme you can turn on energy-group exclusions to get this
> > working, but of course all of those states are sampling unphysical things
> > from a broken forcefield. That can be OK, but you will have to be able to
> > defend that claim.
> >
> > Mark
> >
> > On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan 
> > wrote:
> >
> > > Hello,
> > >
> > > I am running simulations of two protein domains in tip4p water and
> 0.15M
> > > salt concentration that contain up to 650,000 atoms total. The protein
> > > domains are separated from each other at the start of each simulation
> > and I
> > > am measuring how the distance between them changes over time.
> > >
> > > Now, I need to do the same simulations, but with electrostatics between
> > > proteins and water turned off (with water-water, protein-protein,
> > > ion-water, ion-protein electrostatics remaining). Then I need to repeat
> > > that, but additionally turning off electrostatics between the two
> > domains.
> > > Water-water, ion-water, ion-protein, intra-domain electrostatics should
> > > remain on.
> > >
> > > What will be the best way to do this?
> > >
> > > I am using CHARMM27 force field and the following settings to run the
> > > production simulations:
> > >
> > > integrator  = md
> > > dt  = 0.002
> > > nsteps  = 100 ; 2ns
> > > nstlog  = 1000
> > > nstxout = 5000
> > > nstvout = 5000
> > > nstfout = 5000
> > > nstcalcenergy   = 100
> > > nstenergy   = 1000
> > > ;
> > > cutoff-scheme   = Verlet
> > > nstlist = 20
> > > rlist   = 1.2
> > > coulombtype = pme
> > > rcoulomb= 1.2
> > > vdwtype = Cut-off
> > > vdw-modifier= Force-switch
> > > rvdw_switch = 1.0
> > > rvdw= 1.2
> > > ;
> > > tcoupl  = Nose-Hoover
> > > tc_grps = Protein Non-Protein
> > > tau_t   = 1.0 1.0
> > > ref_t   = 300.0   300.0
> > > ;
> > > pcoupl  = Parrinello-Rahman
> > > pcoupltype  = isotropic
> > > tau_p   = 5.0
> > > compressibility = 4.5e-5
> > > ref_p   = 1.0
> > > ;
> > > constraints = h-bonds
> > > constraint_algorithm= LINCS
> > > continuation= yes
> > > ;
> > > nstcomm = 100
> > > comm_mode   = linear
> > > comm_grps   = Protein Non-Protein
> > > ;
> > > refcoord_scaling= com
> > >
> > >
> > > I have tried to use the energy groups (energygrp-table) to specify
> > > interaction tables between water and protein, where I would set the
> > > electrostatic potential to zero. However, given that energygrp-table
> and
> > > Varlet cutoff-scheme are incompatible, I could not make it work. But it
> > is
> > > possible that I did something wrong.
> > >
> > > Thank you in advance,
> > >
> > > Aram
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Aram Davtyan

Hi Mark,

I am not sure I understood. If I for example say "energygrp-excl = Protein
Water" would not I turn off all the non-bonded interactions between water
and protein? Or did you mean something else?

Thanks,

Aram


> Hi,
>
> In the group scheme you can turn on energy-group exclusions to get this
> working, but of course all of those states are sampling unphysical things
> from a broken forcefield. That can be OK, but you will have to be able to
> defend that claim.
>
> Mark
>
> On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan 
> wrote:
>
> > Hello,
> >
> > I am running simulations of two protein domains in tip4p water and 0.15M
> > salt concentration that contain up to 650,000 atoms total. The protein
> > domains are separated from each other at the start of each simulation
> and I
> > am measuring how the distance between them changes over time.
> >
> > Now, I need to do the same simulations, but with electrostatics between
> > proteins and water turned off (with water-water, protein-protein,
> > ion-water, ion-protein electrostatics remaining). Then I need to repeat
> > that, but additionally turning off electrostatics between the two
> domains.
> > Water-water, ion-water, ion-protein, intra-domain electrostatics should
> > remain on.
> >
> > What will be the best way to do this?
> >
> > I am using CHARMM27 force field and the following settings to run the
> > production simulations:
> >
> > integrator  = md
> > dt  = 0.002
> > nsteps  = 100 ; 2ns
> > nstlog  = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstfout = 5000
> > nstcalcenergy   = 100
> > nstenergy   = 1000
> > ;
> > cutoff-scheme   = Verlet
> > nstlist = 20
> > rlist   = 1.2
> > coulombtype = pme
> > rcoulomb= 1.2
> > vdwtype = Cut-off
> > vdw-modifier= Force-switch
> > rvdw_switch = 1.0
> > rvdw= 1.2
> > ;
> > tcoupl  = Nose-Hoover
> > tc_grps = Protein Non-Protein
> > tau_t   = 1.0 1.0
> > ref_t   = 300.0   300.0
> > ;
> > pcoupl  = Parrinello-Rahman
> > pcoupltype  = isotropic
> > tau_p   = 5.0
> > compressibility = 4.5e-5
> > ref_p   = 1.0
> > ;
> > constraints = h-bonds
> > constraint_algorithm= LINCS
> > continuation= yes
> > ;
> > nstcomm = 100
> > comm_mode   = linear
> > comm_grps   = Protein Non-Protein
> > ;
> > refcoord_scaling= com
> >
> >
> > I have tried to use the energy groups (energygrp-table) to specify
> > interaction tables between water and protein, where I would set the
> > electrostatic potential to zero. However, given that energygrp-table and
> > Varlet cutoff-scheme are incompatible, I could not make it work. But it
> is
> > possible that I did something wrong.
> >
> > Thank you in advance,
> >
> > Aram
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
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Re: [gmx-users] Energy analysis

2017-11-19 Thread Mark Abraham

Hi,

Depends what you mean by "stability." A well designed study could seek to
measure or estimate the difference in the free-energy of folding, but that
would probably require an infeasibly large amount of sampling, and be
highly dependent on the quality of the parameterization of the
metal-protein interactions, for which you would probably need some suitable
experimental data.

Mark

On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb  wrote:

> Hi gromacs users,
>
> I want to calculate the energy for comparative analysis of protein with and
> without metal ion, wherein I would like to determine the influence of metal
> on protein structural stability. I have used gromacs for simulation. Please
> suggest me how to do this kind of analysis? Should i follow a specific
> tutorial?
>
> Amir
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] CgenFF conversion failed

2017-11-19 Thread Justin Lemkul



For those interested, the issue is in the NetworkX 2.0 package for 
Python. Version 1.11 produces correct output, but 2.0 fails. I suspect 
this is the root issue of all the recent complaints about the conversion 
script failing.


Thanks to Albert for helping debug this finally.

-Justin

On 11/19/17 1:40 PM, Albert wrote:

file sent to you private email address.

thx a lot


On 11/19/2017 06:06 PM, Justin Lemkul wrote:



On 11/19/17 11:34 AM, Albert wrote:

Hello,

I generated a ligand.str file from Parachem website. Then, I try to 
convert it to Gromacs format with command line:


>cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff


However, the job always failed with the following messages:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, 
Jul 01 2016, 15:36:53) [GCC]


NOTE2: Please be sure to use the same version of CGenFF in your 
simulations that was used during parameter generation:

--Version of CGenFF detected in  ligand.str : 4.0
--Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 
4.0


NOTE3: In order to avoid duplicated parameters, do NOT select the 
'Include parameters that are already in CGenFF' option when 
uploading a molecule into CGenFF.

Traceback (most recent call last):
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in 
    m.read_charmm_rtp(rtplines,atomtypes)
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 540, in 
read_charmm_rtp

    self.G.add_node(self.natoms, atm[self.natoms])
TypeError: add_node() takes exactly 2 arguments (3 given)


I didn't select the 'Include parameters that are already in CGenFF' 
option when uploading a molecule into CGenFF.




That's not relevant to this error.



Does anybody have any idea how to solve this problem?



I have had this problem reported to me several times, yet I have 
never been able to reproduce it. I am beginning to suspect a bug in 
networkx or some weird versioning issue. If you send me your files 
(.str and .mol2) off-list, I will look at it, but unless I am able to 
reproduce the issue, there's not going to be anything I can do.




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-19 Thread Mark Abraham

Hi,

In the group scheme you can turn on energy-group exclusions to get this
working, but of course all of those states are sampling unphysical things
from a broken forcefield. That can be OK, but you will have to be able to
defend that claim.

Mark

On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan  wrote:

> Hello,
>
> I am running simulations of two protein domains in tip4p water and 0.15M
> salt concentration that contain up to 650,000 atoms total. The protein
> domains are separated from each other at the start of each simulation and I
> am measuring how the distance between them changes over time.
>
> Now, I need to do the same simulations, but with electrostatics between
> proteins and water turned off (with water-water, protein-protein,
> ion-water, ion-protein electrostatics remaining). Then I need to repeat
> that, but additionally turning off electrostatics between the two domains.
> Water-water, ion-water, ion-protein, intra-domain electrostatics should
> remain on.
>
> What will be the best way to do this?
>
> I am using CHARMM27 force field and the following settings to run the
> production simulations:
>
> integrator  = md
> dt  = 0.002
> nsteps  = 100 ; 2ns
> nstlog  = 1000
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstcalcenergy   = 100
> nstenergy   = 1000
> ;
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> coulombtype = pme
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ;
> tcoupl  = Nose-Hoover
> tc_grps = Protein Non-Protein
> tau_t   = 1.0 1.0
> ref_t   = 300.0   300.0
> ;
> pcoupl  = Parrinello-Rahman
> pcoupltype  = isotropic
> tau_p   = 5.0
> compressibility = 4.5e-5
> ref_p   = 1.0
> ;
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein Non-Protein
> ;
> refcoord_scaling= com
>
>
> I have tried to use the energy groups (energygrp-table) to specify
> interaction tables between water and protein, where I would set the
> electrostatic potential to zero. However, given that energygrp-table and
> Varlet cutoff-scheme are incompatible, I could not make it work. But it is
> possible that I did something wrong.
>
> Thank you in advance,
>
> Aram
> --
> Gromacs Users mailing list
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> posting!
>
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>
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>
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Re: [gmx-users] CgenFF conversion failed

2017-11-19 Thread Albert


file sent to you private email address.

thx a lot


On 11/19/2017 06:06 PM, Justin Lemkul wrote:



On 11/19/17 11:34 AM, Albert wrote:

Hello,

I generated a ligand.str file from Parachem website. Then, I try to 
convert it to Gromacs format with command line:


>cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff


However, the job always failed with the following messages:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, 
Jul 01 2016, 15:36:53) [GCC]


NOTE2: Please be sure to use the same version of CGenFF in your 
simulations that was used during parameter generation:

--Version of CGenFF detected in  ligand.str : 4.0
--Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE3: In order to avoid duplicated parameters, do NOT select the 
'Include parameters that are already in CGenFF' option when uploading 
a molecule into CGenFF.

Traceback (most recent call last):
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in 
m.read_charmm_rtp(rtplines,atomtypes)
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 540, in 
read_charmm_rtp

self.G.add_node(self.natoms, atm[self.natoms])
TypeError: add_node() takes exactly 2 arguments (3 given)


I didn't select the 'Include parameters that are already in CGenFF' 
option when uploading a molecule into CGenFF.




That's not relevant to this error.



Does anybody have any idea how to solve this problem?



I have had this problem reported to me several times, yet I have never 
been able to reproduce it. I am beginning to suspect a bug in networkx 
or some weird versioning issue. If you send me your files (.str and 
.mol2) off-list, I will look at it, but unless I am able to reproduce 
the issue, there's not going to be anything I can do.


--
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] CgenFF conversion failed

2017-11-19 Thread Justin Lemkul




On 11/19/17 11:34 AM, Albert wrote:

Hello,

I generated a ligand.str file from Parachem website. Then, I try to 
convert it to Gromacs format with command line:


>cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff


However, the job always failed with the following messages:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, 
Jul 01 2016, 15:36:53) [GCC]


NOTE2: Please be sure to use the same version of CGenFF in your 
simulations that was used during parameter generation:

--Version of CGenFF detected in  ligand.str : 4.0
--Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE3: In order to avoid duplicated parameters, do NOT select the 
'Include parameters that are already in CGenFF' option when uploading 
a molecule into CGenFF.

Traceback (most recent call last):
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in 
    m.read_charmm_rtp(rtplines,atomtypes)
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 540, in 
read_charmm_rtp

    self.G.add_node(self.natoms, atm[self.natoms])
TypeError: add_node() takes exactly 2 arguments (3 given)


I didn't select the 'Include parameters that are already in CGenFF' 
option when uploading a molecule into CGenFF.




That's not relevant to this error.



Does anybody have any idea how to solve this problem?



I have had this problem reported to me several times, yet I have never 
been able to reproduce it. I am beginning to suspect a bug in networkx 
or some weird versioning issue. If you send me your files (.str and 
.mol2) off-list, I will look at it, but unless I am able to reproduce 
the issue, there's not going to be anything I can do.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Determining the cut offs more than half of the box

2017-11-19 Thread Justin Lemkul




On 11/19/17 3:17 AM, Iman Ahmadabadi wrote:

Dear Mr.Mark Abraham,

Thank you for your help.
Because of the accuracy of the results, I should use a reasonable cut offs
for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
small for my project because of the importance of long range interactions.


What force field are you using? I know of none that require a 2.0-nm 
cutoff. Note that longer cutoffs do not necessarily provide you with 
greater accuracy (in fact, it can make results worse, depending on the 
force field and the components of the system).



The box size is an obstacle to determining the desired cut off for
interactions.


What you're fighting against is the minimum image convention - the 
shortest box vector must be at least twice as large as the longest 
cutoff to avoid double-counting of forces. If you have a convincing 
reason to use a 2.0-nm cutoff, then the absolute minimum size your box 
must be is 4.0 nm in all directions, but you should construct a box 
larger than that if using pressure coupling, because fluctuations in 
pressure can cause the box size to decrease. If you go below 4.0 nm 
exactly, mdrun will fail.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] CgenFF conversion failed

2017-11-19 Thread Albert


Hello,

I generated a ligand.str file from Parachem website. Then, I try to 
convert it to Gromacs format with command line:


>cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff


However, the job always failed with the following messages:

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Jul 
01 2016, 15:36:53) [GCC]


NOTE2: Please be sure to use the same version of CGenFF in your 
simulations that was used during parameter generation:

--Version of CGenFF detected in  ligand.str : 4.0
--Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc : 4.0

NOTE3: In order to avoid duplicated parameters, do NOT select the 
'Include parameters that are already in CGenFF' option when uploading a 
molecule into CGenFF.

Traceback (most recent call last):
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in 
m.read_charmm_rtp(rtplines,atomtypes)
  File "/home/albert/bin/cgenff_charmm2gmx.py", line 540, in 
read_charmm_rtp

self.G.add_node(self.natoms, atm[self.natoms])
TypeError: add_node() takes exactly 2 arguments (3 given)


I didn't select the 'Include parameters that are already in CGenFF' 
option when uploading a molecule into CGenFF.



Does anybody have any idea how to solve this problem?

Thanks a lot

Albert

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Re: [gmx-users] Determining the cut offs more than half of the box

2017-11-19 Thread Iman Ahmadabadi

Dear Mr.Mark Abraham,

Thank you for your help.
Because of the accuracy of the results, I should use a reasonable cut offs
for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
small for my project because of the importance of long range interactions.
The box size is an obstacle to determining the desired cut off for
interactions.

Best regards

On Sun, Nov 19, 2017 at 11:47 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Mr.Mark Abraham,
>
> Thank you for your help.
> Because of the accuracy of the results, I should use a reasonable cut offs
> for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
> small for my project because of the importance of long range interactions.
> The box size is an obstacle to determining the desired cut off for
> interactions.
>
> Best regards
>
> On Sat, Nov 18, 2017 at 8:37 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs Users,
>>
>> I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
>> that its height along z direction is too small (for example 2.0 nm)  but
>> the error will arise for me and I couldn't use the cut off more than 1.0 nm
>> because of the box size. What should I do in this regard?
>>
>> Best,
>>
>>
>>
>
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Re: [gmx-users] Determining the cut offs more than half of the box

2017-11-19 Thread Iman Ahmadabadi

Dear Mr.Mark Abraham,

Thank you for your help.
Because of the accuracy of the results, I should use a reasonable cut offs
for the interactions around 2.0 nm. The cut offs less than 1.0 nm are too
small for my project because of the importance of long range interactions.
The box size is an obstacle to determining the desired cut off for
interactions.

Best regards

On Sat, Nov 18, 2017 at 8:37 PM, Iman Ahmadabadi  wrote:

> Dear Gromacs Users,
>
> I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
> that its height along z direction is too small (for example 2.0 nm)  but
> the error will arise for me and I couldn't use the cut off more than 1.0 nm
> because of the box size. What should I do in this regard?
>
> Best,
>
>
>

-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Email: imanahmadabad...@gmail.com ,imanahmadab...@physics.sharif.edu

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Re: [gmx-users] mdrun GPU

Re: [gmx-users] Energy analysis

[gmx-users] mdrun GPU

Re: [gmx-users] Energy analysis

Re: [gmx-users] Energy analysis

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] Energy analysis

Re: [gmx-users] CgenFF conversion failed

Re: [gmx-users] Turning off electrostatics between protein and water, then protein and protein

Re: [gmx-users] CgenFF conversion failed

Re: [gmx-users] CgenFF conversion failed

Re: [gmx-users] Determining the cut offs more than half of the box

[gmx-users] CgenFF conversion failed

Re: [gmx-users] Determining the cut offs more than half of the box

Re: [gmx-users] Determining the cut offs more than half of the box

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