- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Wed, 15 Aug 2007 11:52:27 -0400

On 8/15/07, Sudha Mani Karra <karra.md.gmail.com> wrote:

*> Hey Carlos,
*

*> Thank you.
*

*> If you are familiar with the distance restraints, could you help me in
*

*> uderstanding the following?
*

*>
*

*> The md input file is
*

*>
*

*> &cntrl
*

*> imin=0, irest=1, ntx=7,.......,
*

*> .........,
*

*> &end
*

*> &rst iat=1, 6, r1=0.0, r2=..., r3=..., r4=...,
*

*> rk2=....,rk3=.....
*

*> &end
*

*> In the above, for simple harmonic restraints we take r1=0.0 ,r2=r3 and r4 to
*

*> be a large value.
*

correct

*> IF my R is say around 8 A then what should be the r2, r3 and r4 values?
*

you mean R is your target distance? then use r2=8, r3=8, r4=100

*> Also the force constants rk2 and rk3? Which force consant should be used in
*

*> calculating the harmonic potential?
*

it depends on how much fluctuation you want, stronger restraints keep it closer

to the r2/r3 values. put in a sample force constant (say 1) and

calculate how much

distance change you can get for ~0.5-1 kcal/mol, which is what you're going

to get at 300K. values of 0.1 to 10 are probably most useful. too

small and it won't

keep it restrained, too large and you'll get instability in the

simulation since the

frequency of the motion will be too fast for the time step.

*> Appreciate your help.
*

*> Sudha
*

*>
*

*>
*

*>
*

Date: Wed, 15 Aug 2007 11:52:27 -0400

On 8/15/07, Sudha Mani Karra <karra.md.gmail.com> wrote:

correct

you mean R is your target distance? then use r2=8, r3=8, r4=100

it depends on how much fluctuation you want, stronger restraints keep it closer

to the r2/r3 values. put in a sample force constant (say 1) and

calculate how much

distance change you can get for ~0.5-1 kcal/mol, which is what you're going

to get at 300K. values of 0.1 to 10 are probably most useful. too

small and it won't

keep it restrained, too large and you'll get instability in the

simulation since the

frequency of the motion will be too fast for the time step.

-- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun Aug 19 2007 - 06:07:09 PDT

Custom Search