[gmx-users] Umbrella sampling

[rose rahmani]

I need to share you sth which just happened;
i run md_pull.mdp in two steps:
 1--1nS( dt= 0.001 nsteps=1000000) ,
 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000)
and The protein was in normal shape in EVERY steps!

BUT as i told you before when i run just once in 2nS (dt=0.001
nsteps=2000000) periodic boundary conditions make the protein look unusual
in for example conf1500.gro?!!!
What happened? I've got really confused?

Thank ou for your attentions

-Rose


On Sun, Dec 3, 2017 at 4:31 PM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

>
>
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> I took 2000 configuration from trajconv. Amino acid is in its normal
>>> shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>>>
>>
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Bo
>>> undary_Conditions
>>
>> I don't know why this doesn't work since yesterday?!!!!...anyway...
>>
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
>
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
>  protein is getting out of box, should i use trjconv for centering?
>
> Thank you for your attentions
>
>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>