Re: [gmx-users] About ligands and metals in specbond.dat

[Justin Lemkul]

On 7/3/19 3:49 AM, Bakary N'tji Diallo wrote:

Hello
I am adding parameters  for a manganese atom in a force field in Gromacs
following the guide here:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
I have a question about step 6: "If the residue involves special
connectivity to other residues, update specbond.dat."
For the coordinating residues GLU and ASP there is no problem. The
manganese atom is also connected to a ligand in the protein for which I may
know the ID (here LC5)
but the ligand may vary in which case it may be difficult to predict the
ID. It is possible to use
a 'wildcard' approach to account for that? I tried XXX without success.
So far my specbond.dat looks like bellow:
   1 17
   2 CYS SG  1   CYS SG  1   0.2 CYS2CYS2
   3 CYS SG  1   HEM FE  2   0.25CYS2HEME
   4 CYS SG  1   HEM CAB 1   0.18CYS2HEME
   5 CYS SG  1   HEM CAC 1   0.18CYS2HEME
   6 HIS NE2 1   HEM FE  1   0.2 HIS1HEME
   7 MET SD  1   HEM FE  1   0.24MET HEME
   8 CO  C   1   HEMEFE  1   0.19CO  HEME
   9 CYM SG  1   CYM SG  1   0.2 CYS2CYS2
  10 MN  MN  6   ASP OD1 1   0.21MN  ASP
  11 MN  MN  6   ASP OD2 1   0.21MN  ASP
  12 MN  MN  6   GLU OE1 1   0.21MN  GLU
  13 MN  MN  6   GLU OE2 1   0.21MN  GLU
  14 MN  MN  6   LC5 O   1   0.21MN  LC5
  15 MN  MN  6   XXX O   1   0.21MN  XXX
  16 MN  MN  6   LC5 O2  1   0.21MN  LC5
  17 MN  MN  6   XXX O2  1   0.21MN  XXX


The specbond.dat file requires real residue names. As you have it, 
pdb2gmx is going to try to match XXX.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Re: [gmx-users] how to visualize gromacs trajectory

[Justin Lemkul]

On 7/3/19 5:27 AM, sunyeping wrote:

Hi, Steph

I used the following command to repair the trajectory:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc 
mol -ur compact

the bond stretching has disappeared, but the subunits of the protein seperate 
from each other. How to deal with this? Would it be useful to repeat the 
trjconv command?


http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow

-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] GPU support on macOS 10.14

[Michael Williams]

Hi Falk,

I actually compiled Gromacs with openCL GPU support on my MacBook Pro (2017) a 
couple months ago (with some help from others on this mailing list). I’ve 
pasted below the cmake settings that worked. You might be able to find more 
details searching the list for that thread... it took me a little while to get 
it working. Definitely worthwhile though. Have a good one,

Mike

cmake .. 
-DCMAKE_INSTALL_PREFIX=/Users/michael/.local/apps/gromacs-2018.5-apple-clang-omp-ocl
 -DCMAKE_LIBRARY_PATH=/Users/michael/.local/lib 
-DCMAKE_INCLUDE_PATH=/Users/michael/.local/include 
-DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ 
-DCMAKE_C_FLAGS="-Xpreprocessor -fopenmp -lomp -L/Users/michael/.local/lib 
-I/Users/michael/.local/include" -DCMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp 
-lomp -L/Users/michael/.local/lib -I/Users/michael/.local/include" 
-DGMX_FFT_LIBRARY=fftw3 -DGMX_GPU=ON -DGMX_USE_OPENCL=ON

My $HOME/.local directory is the prefix I used to install appropriate versions 
of hwloc (1.11.12), libomp (7.0.1), and fftw3 (3.3.8) that I compiled with the 
system’s default clang (in OSX 10.14.3, Mojave). 

> On Jul 3, 2019, at 8:41 AM, Mark Abraham  wrote:
> 
> Hi,
> 
>> On Wed., 3 Jul. 2019, 15:47 Falk Hoffmann,  wrote:
>> 
>> Hi!
>> 
>> I have a question regarding the GPU support of GROMACS for MacOS. The
>> newest MacBooks (after 2015) are equipped with AMD GPUs which means that
>> GROMACS cannot be compiled with CUDA. GROMACS could be compiled with OpenCL
>> until MacOS 10.13. But this is not possible for MacBooks which have been
>> updated to Mojave (10.14) because Apple deprecated OpenCL (and OpenGL) in
>> this OS in favor of Metal2.
>> 
> 
> Indeed Apple deprecated such support, but it is not yet removed and AFAIK
> is still viable for running codes that require them. Apple's own website
> declares many models that support OpenCL, but does not note whether there
> are OS version constraints... I assume that 10.14 and up don't install such
> components by default any more, but I haven't heard that it is impossible
> to do so... Can anyone confirm or deny?
> 
>> Regarding
> 
>> the improved performance of GPUs especially for nonbonded interactions of
>> biomolecules in bigger systems it would be very useful to use the power of
>> the AMD GPUs in the future. Is there any plan to provide support for Metal2
>> in new releases of GROMACS in the near future?
>> 
> 
> It would be wildly unlikely for GROMACS to support a second proprietary
> language, and particularly one that is not used in the HPC sector. I hope a
> way forward will emerge, but all we know now is that it won't be Metal2 :-)
> 
> Mark
> 
> Or is there another way to compile GROMACS with GPU support under
>> MacOS>=10.14? I tried it with OpenCL, but of course it did not work. I
>> could perfectly compile it without GPU support and run it on CPUs only, but
>> this is not my intention.
>> 
>> Kind regards,
>> Falk
>> 
>> BTW: If this email is better placed in the GROMACS developers list, please
>> move it there.
>> --
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Re: [gmx-users] GPU support on macOS 10.14

[Mark Abraham]

Hi,

On Wed., 3 Jul. 2019, 15:47 Falk Hoffmann,  wrote:

> Hi!
>
> I have a question regarding the GPU support of GROMACS for MacOS. The
> newest MacBooks (after 2015) are equipped with AMD GPUs which means that
> GROMACS cannot be compiled with CUDA. GROMACS could be compiled with OpenCL
> until MacOS 10.13. But this is not possible for MacBooks which have been
> updated to Mojave (10.14) because Apple deprecated OpenCL (and OpenGL) in
> this OS in favor of Metal2.
>

Indeed Apple deprecated such support, but it is not yet removed and AFAIK
is still viable for running codes that require them. Apple's own website
declares many models that support OpenCL, but does not note whether there
are OS version constraints... I assume that 10.14 and up don't install such
components by default any more, but I haven't heard that it is impossible
to do so... Can anyone confirm or deny?

> Regarding

> the improved performance of GPUs especially for nonbonded interactions of
> biomolecules in bigger systems it would be very useful to use the power of
> the AMD GPUs in the future. Is there any plan to provide support for Metal2
> in new releases of GROMACS in the near future?
>

It would be wildly unlikely for GROMACS to support a second proprietary
language, and particularly one that is not used in the HPC sector. I hope a
way forward will emerge, but all we know now is that it won't be Metal2 :-)

Mark

Or is there another way to compile GROMACS with GPU support under
> MacOS>=10.14? I tried it with OpenCL, but of course it did not work. I
> could perfectly compile it without GPU support and run it on CPUs only, but
> this is not my intention.
>
> Kind regards,
> Falk
>
> BTW: If this email is better placed in the GROMACS developers list, please
> move it there.
> --
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> posting!
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[gmx-users] GPU support on macOS 10.14

[Falk Hoffmann]

Hi!

 

I have a question regarding the GPU support of GROMACS for MacOS. The newest MacBooks (after 2015) are equipped with AMD GPUs which means that GROMACS cannot be compiled with CUDA. GROMACS could be compiled with OpenCL until MacOS 10.13. But this is not possible for MacBooks which have been updated to Mojave (10.14) because Apple deprecated OpenCL (and OpenGL) in this OS in favor of Metal2. Regarding the improved performance of GPUs especially for nonbonded interactions of biomolecules in bigger systems it would be very useful to use the power of the AMD GPUs in the future. Is there any plan to provide support for Metal2 in new releases of GROMACS in the near future? Or is there another way to compile GROMACS with GPU support under MacOS>=10.14? I tried it with OpenCL, but of course it did not work. I could perfectly compile it without GPU support and run it on CPUs only, but this is not my intention.

 

Kind regards,

Falk

 

BTW: If this email is better placed in the GROMACS developers list, please move it there. 
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Re: [gmx-users] how to visualize gromacs trajectory

[sunyeping]

Hi, Steph

I used the following command to repair the trajectory:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc 
mol -ur compact

the bond stretching has disappeared, but the subunits of the protein seperate 
from each other. How to deal with this? Would it be useful to repeat the 
trjconv command?

Yeping

--
From:Stephani Macalino 
Sent At:2019 Jul. 3 (Wed.) 12:24
To:gromacs 
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hello,
It sounds like you have to fixed broken molecules and have problem with
boundary conditions.
After doing the MD, you need to fix your trajectory first before doing
visualization.
Check this link for a workflow:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


And this:
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
for detailed trjconv command options.
Regards,
Steph


On Wed, 3 Jul 2019 at 12:21, Sun Yeping  wrote:

> Dear all,
>
> I wish to know what is the best way to visualize gromacs trajectory.
>
> When I load a gromacs trajectory into VMD, I find some of the water
> molecules and some part of the protein in the system are streched and the
> structure become weild and cannot be properly analyzed.
>
> I searched google and found there is a gromacs plugin for vmd, but I don't
> know whether it will help improve gromcas trajectory visualization (
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/
> ).
>
> I also found there is a gromcas plugin for pymol (
> https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems
> to be used for simulation. It doesn't seem to be used to load and visualize
> a extraneous the gromacs trajectory.
>
> What are your suggestion？ Thank you in advance.
>
> Yeping
> --
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Re: [gmx-users] how to visualize gromacs trajectory

[sunyeping]

--
From:孙业平 
Sent At:2019 Jul. 3 (Wed.) 17:27
To:gromacs 
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hi, Steph

I used the following command to repair the trajectory:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc 
mol -ur compact

the bond stretching has disappeared, but the subunits of the protein seperate 
from each other. How to deal with this? Would it be useful to repeat the 
trjconv command?

Yeping
--
From:Stephani Macalino 
Sent At:2019 Jul. 3 (Wed.) 12:24
To:gromacs 
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hello,
It sounds like you have to fixed broken molecules and have problem with
boundary conditions.
After doing the MD, you need to fix your trajectory first before doing
visualization.
Check this link for a workflow:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


And this:
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
for detailed trjconv command options.
Regards,
Steph


On Wed, 3 Jul 2019 at 12:21, Sun Yeping  wrote:

> Dear all,
>
> I wish to know what is the best way to visualize gromacs trajectory.
>
> When I load a gromacs trajectory into VMD, I find some of the water
> molecules and some part of the protein in the system are streched and the
> structure become weild and cannot be properly analyzed.
>
> I searched google and found there is a gromacs plugin for vmd, but I don't
> know whether it will help improve gromcas trajectory visualization (
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/
> ).
>
> I also found there is a gromcas plugin for pymol (
> https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems
> to be used for simulation. It doesn't seem to be used to load and visualize
> a extraneous the gromacs trajectory.
>
> What are your suggestion？ Thank you in advance.
>
> Yeping
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[Vikas Dubey]

Dear all,

I have been trying to use gmx gangle for the calculation of the following
angle :
I have a group of 3 residues and another group of 4 residues. I want to
define a vector which goes through the center of mass of these two groups
and I am interested in calculating the angle  of the vector w.r.t to the
Z-axis, which seems doable from the gmx gangle.
based on the documentation, I write the following :

*gmx angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z -group1
 -seltype res_com
-selrpos -res_com -oav -all   *

but I don't think this is correct because I am calculating the center of
mass of whole group. Is there a way to calculate this angle?

Thanks,
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Re: [gmx-users] carbon dioxide model does not provide valid ideal-gas pressure

[Amin Rouy]

I should add that the problem occurs only in NPT simulation, not in NVT. It
is not only about ideal-gas case, the pressure is not correct for
interactive case too, as soon as it couples to barostat.

On Wed, Jul 3, 2019 at 10:19 AM Amin Rouy  wrote:

> Hi,
>
> I work with carbon dioxide topology modeled by Justin in his tutorial
> page. For a very simple case, I try it with zero charge and zero
> interaction and expect the ideal-gas equation of state to be occurred. But
> it does not. To my trial and errors it seems the pressure is calculated
> with a bug.
>
> Thanks if someone can comment,
>
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[gmx-users] carbon dioxide model does not provide valid ideal-gas pressure

[Amin Rouy]

Hi,

I work with carbon dioxide topology modeled by Justin in his tutorial page.
For a very simple case, I try it with zero charge and zero interaction and
expect the ideal-gas equation of state to be occurred. But it does not. To
my trial and errors it seems the pressure is calculated with a bug.

Thanks if someone can comment,
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Re: [gmx-users] a99SB-disp forcefield

[João Henriques]

Yes. E-mail him directly.

J

On Wed, Jul 3, 2019 at 8:48 AM Timofey Tyugashev 
wrote:

> Paul as Paul Robustelli, the paper author?
>
> 02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
> > Message: 3
> > Date: Tue, 2 Jul 2019 09:52:04 +0200
> > From: Jo?o Henriques
> > To:gmx-us...@gromacs.org, "Greener, Joe"
> > Subject: Re: [gmx-users] a99SB-disp forcefield
> > Message-ID:
> >zu-3jypzd3tsxy...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Ask Paul, they have a Gromacs version of it and he'll most likely be
> happy
> > to share it with you.
> >
> > J
> >
> > On Mon, Jul 1, 2019 at 8:19 PM Joe Greener  wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I am looking to use the a99SB-disp forcefield from Robustelli et al.
> >> PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs
> 2019.3.
> >>
> >> The details of the forcefield are in the paper supplementary material. I
> >> have carried out the following steps:
> >> - Downloaded the Amber99SB*-ILDN-Q forcefield from
> >> http://www.gromacs.org/Downloads/User_contributions/Force_fields  as
> >> ff99sb-star-ildn-q.tgz.
> >> - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
> >> and extracted the water files.
> >> - Modified the water parameters to match a99SB-disp and created a
> >> pre-equilibrated water box.
> >> - Modified the partial charges on certain residues as required.
> >>
> >> Two steps remain that I could do with some advice on:
> >>
> >> - The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
> >> k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
> >> to 1.0. I have looked at the list of dihedral types in the Gromacs
> >> manual and can't find which type these correspond to, or how to convert
> >> the values to a valid dihedral format. I guess this format is the one
> >> used by Desmond.
> >> - The a99SB-disp forcefield has a non-bonded LJ override between all
> >> backbone carbonyl oxygens and amide hydrogens. It seems I could have an
> >> entry something like this in the forcefield files:
> >>
> >> [ nonbond_params ]
> >> O H1sigma_val   epsilon_val
> >>
> >> Would this be sufficient to add this constraint?
> >>
> >> Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
> >> If not I'm happy to make it available if I get it working.
> >>
> >> Best,
> >> Joe
> >>
> >> Joe Greener
> >> Research Associate, UCL
> >> http://jgreener64.github.io/
> >>
> >> --
> >> 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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> >> send a mail togmx-users-requ...@gromacs.org.
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[gmx-users] About ligands and metals in specbond.dat

[Bakary N'tji Diallo]

Hello
I am adding parameters  for a manganese atom in a force field in Gromacs
following the guide here:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
I have a question about step 6: "If the residue involves special
connectivity to other residues, update specbond.dat."
For the coordinating residues GLU and ASP there is no problem. The
manganese atom is also connected to a ligand in the protein for which I may
know the ID (here LC5)
but the ligand may vary in which case it may be difficult to predict the
ID. It is possible to use
a 'wildcard' approach to account for that? I tried XXX without success.
So far my specbond.dat looks like bellow:
  1 17
  2 CYS SG  1   CYS SG  1   0.2 CYS2CYS2
  3 CYS SG  1   HEM FE  2   0.25CYS2HEME
  4 CYS SG  1   HEM CAB 1   0.18CYS2HEME
  5 CYS SG  1   HEM CAC 1   0.18CYS2HEME
  6 HIS NE2 1   HEM FE  1   0.2 HIS1HEME
  7 MET SD  1   HEM FE  1   0.24MET HEME
  8 CO  C   1   HEMEFE  1   0.19CO  HEME
  9 CYM SG  1   CYM SG  1   0.2 CYS2CYS2
 10 MN  MN  6   ASP OD1 1   0.21MN  ASP
 11 MN  MN  6   ASP OD2 1   0.21MN  ASP
 12 MN  MN  6   GLU OE1 1   0.21MN  GLU
 13 MN  MN  6   GLU OE2 1   0.21MN  GLU
 14 MN  MN  6   LC5 O   1   0.21MN  LC5
 15 MN  MN  6   XXX O   1   0.21MN  XXX
 16 MN  MN  6   LC5 O2  1   0.21MN  LC5
 17 MN  MN  6   XXX O2  1   0.21MN  XXX

Best regards

-- 

Bakary N’tji DIALLO

PhD Student (Bioinformatics) , Research
Unit in Bioinformatics (RUBi) 

Mail: diallobaka...@gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14
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Re: [gmx-users] how to visualize gromacs trajectory

[atb files]

Use “dynamic bonding” option from VMD, you can access it by vmd >> 
graphics >> representations >> drawing method >> choose DynamicBonds.Other way 
is make trajectory whole at every time stamp.RunGmx trjconv -f input.gro -o 
output.gro -s input.tpr -pbc mol Gmx trjconv -f input.xtc -o output.xtc -s 
input.tpr -pbc mol Then runVmd output.gro output.xtcDone-YogeshSent using Zoho 
Mail On Wed, 03 Jul 2019 09:53:05 +0530  Stephani 
Macalino wrote Hello,It sounds like you have to 
fixed broken molecules and have problem withboundary conditions.After doing the 
MD, you need to fix your trajectory first before doingvisualization.Check this 
link for a 
workflow:http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_ConditionsAnd
 
this:http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.htmlfor
 detailed trjconv command options.Regards,StephOn Wed, 3 Jul 2019 at 12:21, Sun 
Yeping  wrote:> Dear all,>> I wish to know what is the 
best way to visualize gromacs trajectory.>> When I load a gromacs trajectory 
into VMD, I find some of the water> molecules and some part of the protein in 
the system are streched and the> structure become weild and cannot be properly 
analyzed.>> I searched google and found there is a gromacs plugin for vmd, but 
I don't> know whether it will help improve gromcas trajectory visualization (>> 
https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/> 
).>> I also found there is a gromcas plugin for pymol (> 
https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems> to 
be used for simulation. It doesn't seem to be used to load and visualize> a 
extraneous the gromacs trajectory.>> What are your suggestion？ Thank you in 
advance.>> Yeping> --> 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 
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[gmx-users] How to do proper NVE simulation using Gromacs

[atb files]

Hello,I am trying to do NVE simulation, for that I am first 
properly equilibrating the system by energy minimisation and long NVT, NPT 
simulations. For NVE I set the thermostat and barostat to No. Ideally, the 
systems total energy should not change, but my system energy is gradually 
decreasing and after long run everything is freezing, temperature and all three 
energies (KE, PE and TE) are reducing. What might be the problem, please help- 
Yogesh Sent using Zoho Mail








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Re: [gmx-users] a99SB-disp forcefield

[Timofey Tyugashev]

Paul as Paul Robustelli, the paper author?

02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Tue, 2 Jul 2019 09:52:04 +0200
From: Jo?o Henriques
To:gmx-us...@gromacs.org, "Greener, Joe"
Subject: Re: [gmx-users] a99SB-disp forcefield
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Ask Paul, they have a Gromacs version of it and he'll most likely be happy
to share it with you.

J

On Mon, Jul 1, 2019 at 8:19 PM Joe Greener  wrote:


Dear Gromacs users,

I am looking to use the a99SB-disp forcefield from Robustelli et al.
PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3.

The details of the forcefield are in the paper supplementary material. I
have carried out the following steps:
- Downloaded the Amber99SB*-ILDN-Q forcefield from
http://www.gromacs.org/Downloads/User_contributions/Force_fields  as
ff99sb-star-ildn-q.tgz.
- Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
and extracted the water files.
- Modified the water parameters to match a99SB-disp and created a
pre-equilibrated water box.
- Modified the partial charges on certain residues as required.

Two steps remain that I could do with some advice on:

- The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
to 1.0. I have looked at the list of dihedral types in the Gromacs
manual and can't find which type these correspond to, or how to convert
the values to a valid dihedral format. I guess this format is the one
used by Desmond.
- The a99SB-disp forcefield has a non-bonded LJ override between all
backbone carbonyl oxygens and amide hydrogens. It seems I could have an
entry something like this in the forcefield files:

[ nonbond_params ]
O H1sigma_val   epsilon_val

Would this be sufficient to add this constraint?

Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
If not I'm happy to make it available if I get it working.

Best,
Joe

Joe Greener
Research Associate, UCL
http://jgreener64.github.io/

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