Re: [gmx-users] Drude force field

[Justin Lemkul]

On 7/20/19 12:26 AM, Myunggi Yi wrote:

Dear Justin,

I've followed the instructions, and I prepared my system.

I've got the following error message.

" No default Bond types."

There are several errors.

The bond is between atoms 43 and 45, and the following is a part of the
dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff

 43 OD30CL  1   DMPCO21 43 1.484715.5994   ;
qtot 1.803
 44   DRUD  1   DMPC   DO21 44-1.4847  0   ;
qtot 0.318
 45LPD  1   DMPC   LPMA 45  -0.17  0   ;
qtot 0.148
 46LPD  1   DMPC   LPMB 46  -0.17  0   ;
qtot -0.022
 47 CD2O3B  1   DMPCC21 472.72816 11.611   ;
qtot 2.706
 48   DRUD  1   DMPC   DC21 48   -2.03116  0   ;
qtot 0.675

It seems gromacs added a bond to them, which is not available in the
dmpc.itp file.
Is it common the bond between polar heavy atom and the lone pair virtual
sites?


There should be no bonds to lone pairs. It seems there is an error in 
the .rtp entry for the lipid. The conversion script I used explicitly 
removes these but clearly there is some kind of bug that's not catching 
this. I will look into it. For now, simply remove any LP references in 
[bonds] and regenerate the topology.



Program information:
GROMACS:  gmx grompp, version 2016-dev-20181220-a2cab74

Command line:
   gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr


In addition, I do have not integer total charge.

NOTE 2 [file topol.top, line 49]:
   System has non-zero total charge: -0.000464

Of course, when I generate the protein itp, the total charge was 0.00.
As you know DMPC is neutral too.
After combine protein, dmpc, water, this happened.


That's just rounding error. You're going to encounter this a lot due to 
the large number of fractionally charged particles in a polarizable 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] Drude force field

[Myunggi Yi]

Dear Justin,

I've followed the instructions, and I prepared my system.

I've got the following error message.

" No default Bond types."

There are several errors.

The bond is between atoms 43 and 45, and the following is a part of the
dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff

43 OD30CL  1   DMPCO21 43 1.484715.5994   ;
qtot 1.803
44   DRUD  1   DMPC   DO21 44-1.4847  0   ;
qtot 0.318
45LPD  1   DMPC   LPMA 45  -0.17  0   ;
qtot 0.148
46LPD  1   DMPC   LPMB 46  -0.17  0   ;
qtot -0.022
47 CD2O3B  1   DMPCC21 472.72816 11.611   ;
qtot 2.706
48   DRUD  1   DMPC   DC21 48   -2.03116  0   ;
qtot 0.675

It seems gromacs added a bond to them, which is not available in the
dmpc.itp file.
Is it common the bond between polar heavy atom and the lone pair virtual
sites?

Program information:
GROMACS:  gmx grompp, version 2016-dev-20181220-a2cab74

Command line:
  gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr


In addition, I do have not integer total charge.

NOTE 2 [file topol.top, line 49]:
  System has non-zero total charge: -0.000464

Of course, when I generate the protein itp, the total charge was 0.00.
As you know DMPC is neutral too.
After combine protein, dmpc, water, this happened.

Any suggestion?

Thank you.


On Thu, Jul 18, 2019 at 11:22 AM Justin Lemkul  wrote:

> On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi  wrote:
>
> > Thank you Dr. Lemkel,
> >
> > I don't have ions in my simulation. It's a neutral system with a protein
> in
> > membrane bilayer with solvent.
> > I have downloaded the force field (Drude FF for charmm FF in Gromacs
> > format). to run the simulation with charmm FF in "Gromacs 2019.3".
> > However, it seems the format of the file does not match with the current
> > version.
> >
> > In the web,
> >
> > Compile and install as you would any other (post-5.0) GROMACS version. If
> > you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
> > not be accessible.*
> >
> > There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?
> >
> > Or, it there a way to modify the force field format to use the current
> > version of Gromacs?, Then I will modify the format.
> >
> >
> Read the information at the previous link more carefully. You cannot use
> any released version of GROMACS. You must use the developmental version as
> instructed in that link.
>
> -Justin
>
>
> >
> > On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > > > Dear users,
> > > >
> > > > I want to run a simulation with a polarizable force field.
> > > >
> > > > How and where can I get Drude force field for the current version of
> > > > Gromacs?
> > >
> > > Everything you need to know:
> > >
> > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> > >
> > > The implementation is not complete. If your system has ions, do not use
> > > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> > > OpenMM. The Drude model is still considered experimental, hence it is
> > > not officially supported yet. There have been a lot of snags along the
> > > way (mostly in my time to get the code up to par for official
> inclusion).
> > >
> > > -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
> > >
> > > ==
> > >
> > > --
> > > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
>
> ==
>
> 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
> 

Re: [gmx-users] Drude force field

[Justin Lemkul]

On Thu, Jul 18, 2019 at 4:23 AM Gordan Horvat  wrote:

> I have found this in the NAMD manual:
>
> NAMD has the ability to load GROMACS ASCII topology (.top) and
> coordinate (.gro) files, which allows you to run most GROMACS
> simulations in NAMD.
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node14.html
>
> Is that applicable to the Drude input files prepared by the Gromacs
> Drude distribution?
>

No. To do Drude polarizable simulations in NAMD, you need a CHARMM PSF.

-Justin


> Gordan
>
> --
> Gordan Horvat
> Division of Physical Chemistry
> Department of Chemistry
> Faculty of Science, University of Zagreb
> Croatia
>
> On 18.7.2019. 08:33, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> wrote:
> > On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi
> wrote:
> >
> >> >Thank you Dr. Lemkel,
> >> >
> >> >I don't have ions in my simulation. It's a neutral system with a
> protein in
> >> >membrane bilayer with solvent.
> >> >I have downloaded the force field (Drude FF for charmm FF in Gromacs
> >> >format). to run the simulation with charmm FF in "Gromacs 2019.3".
> >> >However, it seems the format of the file does not match with the
> current
> >> >version.
> >> >
> >> >In the web,
> >> >
> >> >Compile and install as you would any other (post-5.0) GROMACS version.
> If
> >> >you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features
> will
> >> >not be accessible.*
> >> >
> >> >There are 5.0 and 5.1 series of Gromacs versions. Which one should I
> use?
> >> >
> >> >Or, it there a way to modify the force field format to use the current
> >> >version of Gromacs?, Then I will modify the format.
> >> >
> >> >
> > Read the information at the previous link more carefully. You cannot use
> > any released version of GROMACS. You must use the developmental version
> as
> > instructed in that link.
> >
> > -Justin
> >
> >
> >> >
> >> >On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:
> >> >
> >>> > >
> >>> > >
> >>> > >On 7/17/19 8:39 PM, Myunggi Yi wrote:
>  > > >Dear users,
>  > > >
>  > > >I want to run a simulation with a polarizable force field.
>  > > >
>  > > >How and where can I get Drude force field for the current
> version of
>  > > >Gromacs?
> >>> > >
> >>> > >Everything you need to know:
> >>> > >
> >>> > >http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> >>> > >
> >>> > >The implementation is not complete. If your system has ions, do not
> use
> >>> > >GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM,
> or
> >>> > >OpenMM. The Drude model is still considered experimental, hence it
> is
> >>> > >not officially supported yet. There have been a lot of snags along
> the
> >>> > >way (mostly in my time to get the code up to par for official
> inclusion).
> >>> > >
> >>> > >-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
> >>> > >
> >>> > >==
> >>> > >
> >>> > >--
> >>> > >Gromacs Users mailing list
> >>> > >
> >>> > >* Please search the archive at
> >>> > >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List  before
> >>> > >posting!
> >>> > >
> >>> > >* Can't post? Readhttp://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 togmx-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? Readhttp://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 togmx-users-requ...@gromacs.org.
> >> >
> > -- == 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 ==
>
>
> --
> 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.
>
-- 

==

Justin A. Lemkul, Ph.D.

Re: [gmx-users] Drude force field

[Gordan Horvat]

I have found this in the NAMD manual:

NAMD has the ability to load GROMACS ASCII topology (.top) and 
coordinate (.gro) files, which allows you to run most GROMACS 
simulations in NAMD.

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node14.html

Is that applicable to the Drude input files prepared by the Gromacs 
Drude distribution?


Gordan

--
Gordan Horvat
Division of Physical Chemistry
Department of Chemistry
Faculty of Science, University of Zagreb
Croatia

On 18.7.2019. 08:33, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
wrote:

On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi  wrote:


>Thank you Dr. Lemkel,
>
>I don't have ions in my simulation. It's a neutral system with a protein in
>membrane bilayer with solvent.
>I have downloaded the force field (Drude FF for charmm FF in Gromacs
>format). to run the simulation with charmm FF in "Gromacs 2019.3".
>However, it seems the format of the file does not match with the current
>version.
>
>In the web,
>
>Compile and install as you would any other (post-5.0) GROMACS version. If
>you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
>not be accessible.*
>
>There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?
>
>Or, it there a way to modify the force field format to use the current
>version of Gromacs?, Then I will modify the format.
>
>

Read the information at the previous link more carefully. You cannot use
any released version of GROMACS. You must use the developmental version as
instructed in that link.

-Justin



>
>On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:
>

> >
> >
> >On 7/17/19 8:39 PM, Myunggi Yi wrote:

> > >Dear users,
> > >
> > >I want to run a simulation with a polarizable force field.
> > >
> > >How and where can I get Drude force field for the current version of
> > >Gromacs?

> >
> >Everything you need to know:
> >
> >http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> >
> >The implementation is not complete. If your system has ions, do not use
> >GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> >OpenMM. The Drude model is still considered experimental, hence it is
> >not officially supported yet. There have been a lot of snags along the
> >way (mostly in my time to get the code up to par for official inclusion).
> >
> >-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
> >
> >==
> >
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List  before
> >posting!
> >
> >* Can't post? Readhttp://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 togmx-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? Readhttp://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 togmx-users-requ...@gromacs.org.
>
-- == 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] Drude force field

[Justin Lemkul]

On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi  wrote:

> Thank you Dr. Lemkel,
>
> I don't have ions in my simulation. It's a neutral system with a protein in
> membrane bilayer with solvent.
> I have downloaded the force field (Drude FF for charmm FF in Gromacs
> format). to run the simulation with charmm FF in "Gromacs 2019.3".
> However, it seems the format of the file does not match with the current
> version.
>
> In the web,
>
> Compile and install as you would any other (post-5.0) GROMACS version. If
> you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
> not be accessible.*
>
> There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?
>
> Or, it there a way to modify the force field format to use the current
> version of Gromacs?, Then I will modify the format.
>
>
Read the information at the previous link more carefully. You cannot use
any released version of GROMACS. You must use the developmental version as
instructed in that link.

-Justin


>
> On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:
>
> >
> >
> > On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > > Dear users,
> > >
> > > I want to run a simulation with a polarizable force field.
> > >
> > > How and where can I get Drude force field for the current version of
> > > Gromacs?
> >
> > Everything you need to know:
> >
> > http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> >
> > The implementation is not complete. If your system has ions, do not use
> > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> > OpenMM. The Drude model is still considered experimental, hence it is
> > not officially supported yet. There have been a lot of snags along the
> > way (mostly in my time to get the code up to par for official inclusion).
> >
> > -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
> >
> > ==
> >
> > --
> > 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.
>
-- 

==

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] Drude force field

[Myunggi Yi]

I've got the following Error.

It seems this version of Gromacs does not recognize the Drude force field
format distributed by MacKerell.

There are additional Terms like [anisotropic_polarization] , etc..
Gromacs read this as a residue name.




Program gmx, VERSION 5.0.7
Source code file:
/data/cluster/apps/gromacs/source/gromacs-5.0.7/src/gromacs/gmxpreprocess/resall.c,
line: 488

Fatal error:
in .rtp file in residue anisotropic_polarization at line:
 DBR6   BR6C6C1C5 1.8000 0.6000 0.6000




On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:

>
>
> On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > Dear users,
> >
> > I want to run a simulation with a polarizable force field.
> >
> > How and where can I get Drude force field for the current version of
> > Gromacs?
>
> Everything you need to know:
>
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
>
> The implementation is not complete. If your system has ions, do not use
> GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> OpenMM. The Drude model is still considered experimental, hence it is
> not officially supported yet. There have been a lot of snags along the
> way (mostly in my time to get the code up to par for official inclusion).
>
> -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
>
> ==
>
> --
> 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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Re: [gmx-users] Drude force field

[Myunggi Yi]

Thank you Dr. Lemkel,

I don't have ions in my simulation. It's a neutral system with a protein in
membrane bilayer with solvent.
I have downloaded the force field (Drude FF for charmm FF in Gromacs
format). to run the simulation with charmm FF in "Gromacs 2019.3".
However, it seems the format of the file does not match with the current
version.

In the web,

Compile and install as you would any other (post-5.0) GROMACS version. If
you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will
not be accessible.*

There are 5.0 and 5.1 series of Gromacs versions. Which one should I use?

Or, it there a way to modify the force field format to use the current
version of Gromacs?, Then I will modify the format.



On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:

>
>
> On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > Dear users,
> >
> > I want to run a simulation with a polarizable force field.
> >
> > How and where can I get Drude force field for the current version of
> > Gromacs?
>
> Everything you need to know:
>
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
>
> The implementation is not complete. If your system has ions, do not use
> GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> OpenMM. The Drude model is still considered experimental, hence it is
> not officially supported yet. There have been a lot of snags along the
> way (mostly in my time to get the code up to par for official inclusion).
>
> -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
>
> ==
>
> --
> 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] Drude force field

[Myunggi Yi]

Thank you.


On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul  wrote:

>
>
> On 7/17/19 8:39 PM, Myunggi Yi wrote:
> > Dear users,
> >
> > I want to run a simulation with a polarizable force field.
> >
> > How and where can I get Drude force field for the current version of
> > Gromacs?
>
> Everything you need to know:
>
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
>
> The implementation is not complete. If your system has ions, do not use
> GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or
> OpenMM. The Drude model is still considered experimental, hence it is
> not officially supported yet. There have been a lot of snags along the
> way (mostly in my time to get the code up to par for official inclusion).
>
> -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
>
> ==
>
> --
> 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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Re: [gmx-users] Drude force field

[Justin Lemkul]

On 7/17/19 8:39 PM, Myunggi Yi wrote:

Dear users,

I want to run a simulation with a polarizable force field.

How and where can I get Drude force field for the current version of
Gromacs?


Everything you need to know:

http://mackerell.umaryland.edu/charmm_drude_ff.shtml

The implementation is not complete. If your system has ions, do not use 
GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or 
OpenMM. The Drude model is still considered experimental, hence it is 
not officially supported yet. There have been a lot of snags along the 
way (mostly in my time to get the code up to par for official inclusion).


-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] Drude force field

[Myunggi Yi]

Dear users,

I want to run a simulation with a polarizable force field.

How and where can I get Drude force field for the current version of
Gromacs?

Thank you.
-- 
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[gmx-users] Drude force field

[Myunggi Yi]

Dear users,

How or where can I get the Drude polarizable force field file for current
Gromacs version?
-- 
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Re: [gmx-users] Drude force field

[Justin Lemkul]

On 7/20/17 8:08 AM, Shraddha Parate wrote:

Hi gmx users!

For polarizable effect, I was setting drude force field in Gromacs
I attempted running Lagrangian Dynamics simulation using Drude force field.
mdp file format was used from the supporting data in below paper.

[2015] Implementation of extended Lagrangian dynamics in GROMACS for
polarizable simulations using the classical Drude oscillator model.(
http://onlinelibrary.wiley.com/doi/10.1002/jcc.23937/abstract;jsessionid=E354008D7BE6AA1A02D26C061B49163A.f02t01
)




---

   ; RUN CONTROL PARAMETERS
   integrator = md-vv

   ; Start time and timestep in ps
   tinit = 0
   dt = 0.001
   nsteps = 1
   comm-mode = linear
   nstcomm = 100
   comm-grps = System

   ; OUTPUT CONTROL OPTIONS
   nstxout = 1000
   nstvout = 1000
   nstfout = 1000

   ; Output frequency for energies to log file and energy file
   nstlog = 100
   nstcalcenergy = 100
   nstenergy = 100

   ; NEIGHBORSEARCHING PARAMETERS
   cutoff-scheme = verlet
   nstlist = 10
   ns-type = Grid
   pbc = xyz
   rlist = 1.2

   ; OPTIONS FOR ELECTROSTATICS AND VDW
   coulombtype = PME
   rcoulomb = 1.2
   vdwtype = cutoff
   vdw-modifier = potential-switch
   rvdw-switch = 1.0
   rvdw = 1.2
   DispCorr = EnerPres

   ; TEMPERATURE COUPLING
   tcoupl = Nose-Hoover
   nsttcouple = 1
   nh-chain-length = 1

   ; Groups to couple separately
   tc-grps = Atoms Drues
   tau-t = 0.1 0.005
   ref-t = 298.15 1.0

   ; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO
   ; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED
   gen-vel = yes
   gen-temp = 298.15
   gen-seed = -1

   ; OPTIONS FOR BONDS
   constraints = none ; can also be h-bonds, not all-bonds
   continuation = no


   ; DRUDE PARAMETERS
   drude = yes
   drude-mode = Lagrangian
   drude-t = 1.0
   drude-hardwall = yes
   drude-r = 0.02
   drude-tsteps = 5
---


I couldn't understand [tc-grps = Atoms Drude] option.


All the atoms in one group, all the Drudes in the next.  If you want to break 
the system apart into protein and non-protein:


tc-grps = Protein-Atoms Protein Drudes Non-Protein-Atoms Non-Protein-Drudes
ref_t = 298.15 1.0 298.15 1.0
tau_t = 1.0 0.005 1.0 0.005


If the option is changed to [tc-grps = Protein SOL],I get a fatal error
message.

--
Fatal error:
Incorrect thermostat setup in relative_tstat, ti = -1
--

How to resolve this issue? Why the changed parameter gives a fatal error?



Do what the paper (and the ones cited therein) tell you to do.  The Drude 
integration scheme requires a special dual thermostat that couples the Drude 
oscillators to a low-temperature thermostat to approximate the SCF surface.  You 
can't treat these kinds of systems like you would additive ones.  The atoms 
(anything non-Drude) and Drudes have to be in separate thermostats, in a given 
order, as explained in the paper (and shown above).


Note that domain decomposition remains broken, so you can only run with OpenMP. 
I recently identified the (hopefully) last remaining issue but it will take some 
time to get it fixed as I am currently moving and starting my own lab, so my 
attention is elsewhere for a while.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Drude force field

[Shraddha Parate]

Hi gmx users!

For polarizable effect, I was setting drude force field in Gromacs
I attempted running Lagrangian Dynamics simulation using Drude force field.
mdp file format was used from the supporting data in below paper.

[2015] Implementation of extended Lagrangian dynamics in GROMACS for
polarizable simulations using the classical Drude oscillator model.(
http://onlinelibrary.wiley.com/doi/10.1002/jcc.23937/abstract;jsessionid=E354008D7BE6AA1A02D26C061B49163A.f02t01
)




---

  ; RUN CONTROL PARAMETERS
  integrator = md-vv

  ; Start time and timestep in ps
  tinit = 0
  dt = 0.001
  nsteps = 1
  comm-mode = linear
  nstcomm = 100
  comm-grps = System

  ; OUTPUT CONTROL OPTIONS
  nstxout = 1000
  nstvout = 1000
  nstfout = 1000

  ; Output frequency for energies to log file and energy file
  nstlog = 100
  nstcalcenergy = 100
  nstenergy = 100

  ; NEIGHBORSEARCHING PARAMETERS
  cutoff-scheme = verlet
  nstlist = 10
  ns-type = Grid
  pbc = xyz
  rlist = 1.2

  ; OPTIONS FOR ELECTROSTATICS AND VDW
  coulombtype = PME
  rcoulomb = 1.2
  vdwtype = cutoff
  vdw-modifier = potential-switch
  rvdw-switch = 1.0
  rvdw = 1.2
  DispCorr = EnerPres

  ; TEMPERATURE COUPLING
  tcoupl = Nose-Hoover
  nsttcouple = 1
  nh-chain-length = 1

  ; Groups to couple separately
  tc-grps = Atoms Drues
  tau-t = 0.1 0.005
  ref-t = 298.15 1.0

  ; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO
  ; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED
  gen-vel = yes
  gen-temp = 298.15
  gen-seed = -1

  ; OPTIONS FOR BONDS
  constraints = none ; can also be h-bonds, not all-bonds
  continuation = no


  ; DRUDE PARAMETERS
  drude = yes
  drude-mode = Lagrangian
  drude-t = 1.0
  drude-hardwall = yes
  drude-r = 0.02
  drude-tsteps = 5
---


I couldn't understand [tc-grps = Atoms Drude] option.
If the option is changed to [tc-grps = Protein SOL],I get a fatal error
message.

--
Fatal error:
Incorrect thermostat setup in relative_tstat, ti = -1
--

How to resolve this issue? Why the changed parameter gives a fatal error?

I look forward to your response.
Thank you for reading.
-- 
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Re: [gmx-users] Drude force field

[Justin Lemkul]

On 10/28/16 3:27 PM, Xianchi Dong wrote:

I simply put the ff files to the working folder and used the previous
installed Gromacs 5.1.2.
When use pdb2gmx, it gives the error msg:

Fatal error:
in .rtp file in residue anisotropic_polarization at line:
  DO1O1C1  LP1A  LP1B 0.8108 1.2162 0.9730

Could you give me some advise?



The Drude features are in the "drude" development branch only.  You cannot use 
released GROMACS versions.  See the instructions on the linked page I posted 
earlier.


-Justin


Best,
Xianchi

On Fri, Oct 28, 2016 at 3:17 PM, Justin Lemkul  wrote:




On 10/28/16 2:48 PM, Xianchi Dong wrote:


Thanks for your reply.
Do I need to copy the ff file to any folder?



Either the working directory or $GMXLIB, like any other force field.

-Justin


Best,

Xianchi

On Oct 28, 2016, at 1:56 PM, Justin Lemkul  wrote:




On 10/28/16 1:39 PM, Xianchi Dong wrote:

Dear all,
Does anyone have a detailed protocol to install Drude polarized force
field on Gromacs?



There's nothing special about installation or use:

http://mackerell.umaryland.edu/charmm_drude_ff.shtml

Be aware that runs using domain decomposition may crash due to an as-yet
unresolved bug.  I'm working on it, but it's below certain other priorities
at the moment.  OpenMP runs are fine.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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send a mail to gmx-users-requ...@gromacs.org.




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Drude force field

[Xianchi Dong]

I simply put the ff files to the working folder and used the previous
installed Gromacs 5.1.2.
When use pdb2gmx, it gives the error msg:

Fatal error:
in .rtp file in residue anisotropic_polarization at line:
  DO1O1C1  LP1A  LP1B 0.8108 1.2162 0.9730

Could you give me some advise?

Best,
Xianchi

On Fri, Oct 28, 2016 at 3:17 PM, Justin Lemkul  wrote:

>
>
> On 10/28/16 2:48 PM, Xianchi Dong wrote:
>
>> Thanks for your reply.
>> Do I need to copy the ff file to any folder?
>>
>>
> Either the working directory or $GMXLIB, like any other force field.
>
> -Justin
>
>
> Best,
>> Xianchi
>>
>> On Oct 28, 2016, at 1:56 PM, Justin Lemkul  wrote:
>>>
>>>
>>>
>>> On 10/28/16 1:39 PM, Xianchi Dong wrote:
 Dear all,
 Does anyone have a detailed protocol to install Drude polarized force
 field on Gromacs?


>>> There's nothing special about installation or use:
>>>
>>> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
>>>
>>> Be aware that runs using domain decomposition may crash due to an as-yet
>>> unresolved bug.  I'm working on it, but it's below certain other priorities
>>> at the moment.  OpenMP runs are fine.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> 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.
>>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * 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] Drude force field

[Justin Lemkul]

On 10/28/16 2:48 PM, Xianchi Dong wrote:

Thanks for your reply.
Do I need to copy the ff file to any folder?



Either the working directory or $GMXLIB, like any other force field.

-Justin


Best,
Xianchi


On Oct 28, 2016, at 1:56 PM, Justin Lemkul  wrote:




On 10/28/16 1:39 PM, Xianchi Dong wrote:
Dear all,
Does anyone have a detailed protocol to install Drude polarized force field on 
Gromacs?



There's nothing special about installation or use:

http://mackerell.umaryland.edu/charmm_drude_ff.shtml

Be aware that runs using domain decomposition may crash due to an as-yet 
unresolved bug.  I'm working on it, but it's below certain other priorities at 
the moment.  OpenMP runs are fine.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Drude force field

[Xianchi Dong]

Thanks for your reply.
Do I need to copy the ff file to any folder?

Best,
Xianchi

> On Oct 28, 2016, at 1:56 PM, Justin Lemkul  wrote:
> 
> 
> 
>> On 10/28/16 1:39 PM, Xianchi Dong wrote:
>> Dear all,
>> Does anyone have a detailed protocol to install Drude polarized force field 
>> on Gromacs?
>> 
> 
> There's nothing special about installation or use:
> 
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> 
> Be aware that runs using domain decomposition may crash due to an as-yet 
> unresolved bug.  I'm working on it, but it's below certain other priorities 
> at the moment.  OpenMP runs are fine.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] Drude force field

[Justin Lemkul]

On 10/28/16 1:39 PM, Xianchi Dong wrote:

Dear all,
Does anyone have a detailed protocol to install Drude polarized force field on 
Gromacs?



There's nothing special about installation or use:

http://mackerell.umaryland.edu/charmm_drude_ff.shtml

Be aware that runs using domain decomposition may crash due to an as-yet 
unresolved bug.  I'm working on it, but it's below certain other priorities at 
the moment.  OpenMP runs are fine.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Drude force field

[Xianchi Dong]

Dear all,
Does anyone have a detailed protocol to install Drude polarized force field on 
Gromacs?

Best,
Xianchi
-- 
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