Re: [gmx-users] QM calculation

[mohammad r]

Thank you very much Justin for your helpful answer. 

On Thursday, March 31, 2016 3:40 PM, Justin Lemkul  wrote:
 

 

On 3/31/16 12:19 AM, mohammad r wrote:
> Thank you Justin, I want to do QM calculationbefore running equilibration
> then run the MD simulation by GROMACS. Do you knowwhich software is
> appropriate and compatible with GROMACS that after QM calculation I can run
> the rest of simulation?

Again, for a pure QM calculation (geometry optimization, I presume) there is no 
interaction with GROMACS or any other software.  You do your optimization, 
output the coordinates, and then move on.  If I'm missing some critical detail, 
please describe exactly what you want to do.

-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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Re: [gmx-users] QM calculation

[Justin Lemkul]

On 3/31/16 12:19 AM, mohammad r wrote:

Thank you Justin, I want to do QM calculationbefore running equilibration
then run the MD simulation by GROMACS. Do you knowwhich software is
appropriate and compatible with GROMACS that after QM calculation I can run
the rest of simulation?


Again, for a pure QM calculation (geometry optimization, I presume) there is no 
interaction with GROMACS or any other software.  You do your optimization, 
output the coordinates, and then move on.  If I'm missing some critical detail, 
please describe exactly what you want to do.


-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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Re: [gmx-users] QM calculation

[mohammad r]

Thank you Justin, I want to do QM calculationbefore running equilibration then 
run the MD simulation by GROMACS. Do you knowwhich software is appropriate and 
compatible with GROMACS that after QM calculation I can run the rest of 
simulation?
Best, Mohammad.

On Thursday, March 31, 2016 3:43 AM, Justin Lemkul  wrote:
 

 

On 3/30/16 2:17 AM, mohammad r wrote:
> Hi gromacs users,
>
>
>
> I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
> to gromacs tutorial)? Or I should do it by using gromacsitself? By the way

QM calculations are not reliant on MM topologies, like those from PRODRG (which 
are poor quality anyway) or any force field terms.

GROMACS does not do QM directly, though there are interfaces to popular QM 
codes 
for doing QM/MM.  For strict QM, abandon GROMACS and use the appropriate 
software.

> I’ve generated the initial coordinate and topology files inamber tools then
> convert it to gromacs format by using parmed (because theforce field which I
> want is not included in gromacs).
>

Again, for a pure QM calculation, there is no need for any MM programs or force 
fields.

-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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Re: [gmx-users] QM calculation

[Justin Lemkul]

On 3/30/16 2:17 AM, mohammad r wrote:

Hi gromacs users,



I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
to gromacs tutorial)? Or I should do it by using gromacsitself? By the way


QM calculations are not reliant on MM topologies, like those from PRODRG (which 
are poor quality anyway) or any force field terms.


GROMACS does not do QM directly, though there are interfaces to popular QM codes 
for doing QM/MM.  For strict QM, abandon GROMACS and use the appropriate software.



I’ve generated the initial coordinate and topology files inamber tools then
convert it to gromacs format by using parmed (because theforce field which I
want is not included in gromacs).



Again, for a pure QM calculation, there is no need for any MM programs or force 
fields.


-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] QM calculation

[mohammad r]

Hi gromacs users,


 
I want to do QMcalculation to my system. Can the PRODRG sitedo it (according to 
gromacs tutorial)? Or I should do it by using gromacsitself? By the way I’ve 
generated the initial coordinate and topology files inamber tools then convert 
it to gromacs format by using parmed (because theforce field which I want is 
not included in gromacs).


 
Thank you, Mohammad.

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