[gmx-users] Re: Simulation in the high temperature conditions

Mon Apr 16 16:02:54 CEST 2012

Justin,

Thank you for explanation. Tomorrow I'll try to check results of simulation
with the disres applied with its default values as well as with narrower
-disre_dist values ( ignorring -disre_frac option at all )  and post here
results of such simulations.

1) The cut-off distance wich I've specified was defined with the genrest
comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the
backbone atoms of alpha helices of the Transmembrane domain of my protein
wich I've defined in the index.ndx file. So all loops of my protein were
not-restrained at all.

Also I have some small  question about size of output edr file. I've
noticed that size of this files of such simulations  (with the disres
applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this
occurs and how I could fix it?

thanks again for help,

James

16 апреля 2012 г. 17:36 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>> I've applied disres on each backbone atom of my potein within cutoff
>> distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
>> decrease overall ammount of the restains in my itp file. Also such value (
>> 1nm) was selected because of the relatively tight packing of the alpha
>> helices in the TM buddle of membrane protein.
>>
>>
> I still don't see how you're defining this cutoff anywhere in genrestr or
> any other step.  Do you have some special index group that you're using in
> your genrestr command?  It may not be relevant, I'm just very confused.
>
>
>  The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2
>> and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but
>> I have not noticed any difference in the resulted behaviour of the
>> constrained system. As the consequence I have not clearly realise what
>> exactly is the disre_frac and in what exactly cases this option could be
>> helpfull.
>>
>>
> The -disre_dist option sets the tolerance for defining the 'lo' value.  By
> default, it is a fixed distance below the actual distance contained in the
> coordinate file.  The default value is 0.1, so if your distance is 0.5, the
> 'lo' value is set to 0.4 (i.e. 0.5 - 0.1).  When using the -disre_frac
> value, the value specified in -disre_dist is ignored, so be aware that when
> you combine the two, you override -disre_dist (as stated in genrestr -h).
>  So if you're using -disre_frac of 0.5, your 'lo' value for a 0.5-nm
> distance is 0.25.
>
>
>
>> This is an example of my output itp file
>>
>> [ distance_restraints ]
>> ;   i     j ? label      funct         lo        up1        up2     weight
>>    1     5 1     0          1          0    1.64731    2.64731          1
>>    1    10 1     1          1          0     1.7326     2.7326          1
>>    1    12 1     2          1          0    1.83886    2.83886          1
>>    1    14 1     3          1          0    1.96079    2.96079          1
>>    1    15 1     4          1          0    2.03503    3.03503          1
>>    1    17 1     5          1          0    1.99007    2.99007          1
>>    1    19 1     6          1          0    2.08879    3.08879          1
>>    1    27 1     7          1          0    2.13916    3.13916          1
>>    1    29 1     8          1          0    2.27147    3.27147          1
>>    1    30 1     9          1          0    2.35793    3.35793          1
>>
>>
>> I've made 10 ns simulation of such system and observe rapid shrinking of
>> my protein starting with first 100ps like the distances that I chose were
>> too small and forces shrink my protein. But when I've tried larger distance
>> value for disre_dist my protein denatured rapidly as no disres were
>> presented.
>>
>>
> The problem here is that you're allowing all distances between 0 and 'up1'
> to experience zero restraining force.  That gives the system incredibly
> wide latitude and basically makes the restraints useless.  What you're
> calling either shrinking or denaturing are likely just two possible
> outcomes from the structure being destabilized in some way.  Try running
> genrestr with default options to see if you get a better result.
>
>
>  So the main question is How I could specify this disre values if I want
>> to restrain the motion of the helixes of my protein within disre value (
>> e.g 10 A) relatively current confrmation ?
>>
>>
> Are you wanting the restraints to be maintained within a 1-nm distance of
> their current value?  That's a very wide latitude.  If that's what you
> want, then use the -disre_dist option without -disre_frac.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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