On 2/20/18 12:52 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear Justin
Thank you for the reply
You meant , to tweak the emtol doesn't have noticable affects on the
conformational enssemble generated by MD?
Precisely what I said, yes.
-Justin
Sent from Yahoo Mail for iPhone
On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/20/18 4:52 AM, farial tavakoli wrote:
Dear GMX users
I used CHARMM36 all atom force field to generate .top and .gro files for my
complex composed of a receptor protein and a ligand with 2 phosphotyrosine
residues, then ran a md simulation on it and then used g_mmpbsa to calculate
the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol,
respectively. While, I calculated binding energy before for many other
complexes without any phosphate groups using OPLS all atom force field and pdie
= 2 and obtained minus energy. But this time , I dont know why I got positive
binding energy? Is it because of charmm36 all atom force field , the phosphate
groups or it is needed to be energy minimized under more restriction situations?
I am checking different factors to understand its reason, so I wanted to know ,
would it be ok if I energy minimize the complex with more restriction
situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ?
I think the positive binding energy might be because of the complex didnt
minimized well. however I checked the em.log file and saw it was minimized well:
Steepest Descents converged to Fmax < 1000 in 241 steps
Potential Energy = -6.5047744e+05
Maximum force = 9.8285083e+02 on atom 3335
Norm of force = 3.6905827e+01
Is there anyone can advice me in energy minimization with emtol 800?
The purpose of energy minimization is to establish a reasonable starting
point for your simulation. Tweaks to emtol will have little to no
noticeable bearing on the conformational ensemble generated by MD.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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