[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:
>       DO1    O1    C1  LP1A  LP1B 0.81080000 1.21620000 0.97300000
>
> 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 <jalemkul at 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 <jalemkul at 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
>>>>
>>>> jalemkul at 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
>>
>> jalemkul at 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
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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

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

==================================================