Hi Jason,
Thanks a lot for your email.
1. I went through the generalized distance restraint option.
Thus in order to use it for say, to move an atom close to a set of three atoms,
is the command pasted below correct:
&rst iat=125,300,125,450,125,651 rstwt=1.0,1.0,0.75 r2=55.0, rk2=10, r2a=15.0 /
2. However I am confused when it comes to r2. Should r2 be (d1+d2+d3), d1 to d3
being the corresponding distances between 125 and the other three atoms. Also
what should be the value of r2a ? Should it be (d1'+d2'+d3'), d1' to d3' being
my desired distances after steering between 125 and the three atoms concerned ?
3. Also the value of rk2 varies a lot from the manual to what I see in the
literature. How do I decide on it.
4. Is rk2 equivalent to harm in ncsu. I ask this so that I am effieciently able
to translate my ncsu_smd code to a jar=1 code.
My jar=1 code:
jar=1/
/&wt TYPE='DUMPFREQ', istep1=1, /
&wt TYPE='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
dist.RST being:
&rst iat=125,300,125,450,125,651 rstwt=1.0,1.0,0.75 r2=55.0, rk2=10, r2a=15.0 /
Does this translate to using harm=10 and going from a LCOD of 55ang to LCOD of
15 ang, with LCOD distances being as I had defined above.
Thanks a lot for your reply and would look forward to hear from you.
Best Regards,
Moitrayee
> On Tue, Jun 25, 2013 at 3:23 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
>
>> Dear Amber Users,
>>
>> This is in reference to the tutorial at
>> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/
>>
>>
>> Questions:
>>
>> 1. I understand the LCOD mode was supported in ncsu_smd module which is no
>> longer supported by Amber mailing list. Is there an equivalent when I am
>> using
>> the jar=1 option. This is because I want to have parallel restraints and
>> move an
>> atom close to a set of three atoms.
>>
>
> Yes, there is an equivalent (kind of). It only supports a subset of the
> functionality provided by the NCSU module, but arguably some of the most
> popular functionality.
>
> Look for the 'generalized distance' restraint in Chapter 6 of the Amber
> manual (the NMR restraint section). The relevant variables are iat and
> rstwt. It lets you do a linear combination of up to 4 distances.
>
>
>> 2. I looked into the amber mailing list
>> (http://archive.ambermd.org/200806/0150.html) and in this case is the
>> pulling
>> velocity = 55-15/2ns = 20ang/ns ; 55 ang being my starting LCOD and 15
>> being the
>> endpoint ?
>>
>
> Yes.
>
>
>
>> 3. I am keeping the spring const throughout the run using rk2=1.0725. Is
>> the
>> unit kcal/mol ang^2 ? If so how is it related to the pulling velocity and
>> thermal fluctuations ? Also what is the physical meaning of this value ?
>>
>
> Yes, it is kcal/mol/ang^2. However, the restraint equation is
> U=k[f(s)-s_0] where s_0 is the 'equilibrium' value of the reaction
> coordinate s and f(s) is the actual value of the reaction coordinate
> (notice there is no factor of 1/2 in front of it).
>
> This value is effectively twice the spring constant of the restraint.
> There's no additional 'physical' meaning to this potential since it's a
> biasing potential that's not real (and that you hope to remove later from
> the final PMF).
>
>
>> 4. Is it possible to steer loops in two subunits of a dimeric protein
>> simultaneously. I am confused if this can be done.
>>
>
> Only if both 'steerings' are part of the same reaction coordinate. I
> believe that only one coordinate can be steered at a time using the NMRopt
> code.
>
> 5. I think this script is implementing a const force smd as I fix the value
>> of
>> spring constant. Is this true ?
>>
>
> I may not be familiar with how this terminology is used, but in general
> this will NOT be constant force. It is constant force constant, but the
> force itself will obviously change based on how far away from the
> 'equilibrium' value the conformation happens to be. I actually think
> people call this 'constant velocity' steered MD since the center of the
> steering potential is moved at a constant speed.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Jun 25 2013 - 18:30:03 PDT
