[gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 4:56 AM, roshanak starlight wrote:
> excuse me i forgot that  write subject.
>
> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <starlight.r77 at gmail.com
>> wrote:
>
>> hello
>> i use kalp-15 in dppc tutorial  that there is in this website :
>> http://www.bevanlab.biochem.vt.edu
>> i have 2 question about step 3 :
>> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
>> -fc 100000 100000 100000 which shoud i choose ?    ( i choose 1:protein .
>> is it right ?)

 From the tutorial:

"The authors of the InflateGRO script recommend using a very strong 
position-restraining force on protein heavy atoms to ensure that the position of 
the protein does not change during EM."

So choose the protein heavy atoms (Protein-H).

>> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
>> thank you
>>

It doesn't matter.

-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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