[gmx-users] Drude polarization ff for Ca2+ and Mg2+

2018-08-31 Thread Xianchi Dong
Dear GMX users,
I am wondering where I can find the polarization parameter for Ca2+ and/or
Mg2+ for Gromacs?

Best,
Xianchi
-- 
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] Drude force field

2016-10-28 Thread 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 <jalem...@vt.edu> 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 <jalem...@vt.edu> 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.
>
-- 
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] Drude force field

2016-10-28 Thread 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 <jalem...@vt.edu> 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.
-- 
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.


[gmx-users] Drude force field

2016-10-28 Thread Xianchi Dong
Dear all,
Does anyone have a detailed protocol to install Drude polarized force field on 
Gromacs?

Best,
Xianchi
-- 
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] QMMM install on GMX5.1 (Xianchi Dong)

2016-10-16 Thread Xianchi Dong
Hi Andrew,
Thanks for reply

I tried to configure with cmake, the command I used is cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_PREFIX_PATH=../../mopac_lib/
-DCMAKE_INSTALL_PREFIX=~/Programs/Gromacs-5.1.2/ -DGMX_QMMM_MOPAC=on

When I used make. It prompted with error msg:

Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to `domop_'
../../lib/libgromacs.so.1.2.0: undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

Best,
Xianchi

On Sun, Oct 16, 2016 at 8:37 PM, Andrew Guy <andrew@burnet.edu.au>
wrote:

> Hi Xianchi,
>
> It would be more helpful if you can provide a detailed description of what
> failed when you tried to install QMMM. Just saying it failed doesn't give
> people much insight into how to assist you.
>
> There are a myriad of possibilities, but without an actual error message to
> go off, we're all in the dark here.
>
> Regards,
>
> Andrew
>
> On Mon, Oct 17, 2016 at 11:20 AM, Xianchi Dong <dongxian...@gmail.com>
> wrote:
>
> > Hi Clinton,
> > Thanks a lot for your reply. I tried but still failed.
> > Would you like to say more about how to configure Gromacs 5.1.2 with
> > CPPFLAGS, LIBS, and LDGFLAGS with cmake.
> >
> > Best,
> > Xianchi
> >
> >
> > > On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu
> >
> > wrote:
> > >
> > > Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> > >
> > > You will also need to set the following variable at install time:
> > >
> > > -DGMX_QMMM_MOPAC=ON
> > >
> > > --
> > > Clinton King
> > > Graduate Student
> > > Chemistry Department
> > > Brigham Young University
> > >
> > >
> > >>
> > >>   1. QMMM install on GMX5.1 (Xianchi Dong)
> > >>
> > >>
> > >> Message: 1
> > >> Date: Fri, 14 Oct 2016 17:14:36 -0400
> > >> From: Xianchi Dong <dongxian...@gmail.com>
> > >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> > >> Subject: [gmx-users] QMMM install on GMX5.1
> > >> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
> > >> Content-Type: text/plain; charset=us-ascii
> > >>
> > >> Hi all,
> > >> Does anyone know how to install qmmm code like mopac to gmx5.1?
> > >>
> > >> Best,
> > >> Xianchi
> > >>
> > >>
> > >>
> > > --
> > > 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.
>
-- 
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] QMMM install on GMX5.1 (Xianchi Dong)

2016-10-16 Thread Xianchi Dong
Hi Clinton,
Thanks a lot for your reply. I tried but still failed. 
Would you like to say more about how to configure Gromacs 5.1.2 with CPPFLAGS, 
LIBS, and LDGFLAGS with cmake.

Best,
Xianchi


> On Oct 15, 2016, at 12:52 PM, Clinton King <clintonkin...@chem.byu.edu> wrote:
> 
> Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> 
> You will also need to set the following variable at install time:
> 
> -DGMX_QMMM_MOPAC=ON
> 
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
> 
> 
>> 
>>   1. QMMM install on GMX5.1 (Xianchi Dong)
>> 
>> 
>> Message: 1
>> Date: Fri, 14 Oct 2016 17:14:36 -0400
>> From: Xianchi Dong <dongxian...@gmail.com>
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] QMMM install on GMX5.1
>> Message-ID: <d4d77c48-e81c-4eeb-b75a-d01b10cd9...@gmail.com>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> Hi all,
>> Does anyone know how to install qmmm code like mopac to gmx5.1?
>> 
>> Best,
>> Xianchi
>> 
>> 
>> 
> -- 
> 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.


[gmx-users] QMMM install on GMX5.1

2016-10-14 Thread Xianchi Dong
Hi all,
Does anyone know how to install qmmm code like mopac to gmx5.1?

Best,
Xianchi
-- 
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.