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

From: dhacademic <dhacademic.gmail.com>

Date: Wed, 2 Jun 2010 14:17:57 -0400

Dear Amber users,

I have two questions about the restraint in umbrella sampling.

(1) According to the Amber9 tutorial (p159), the torsion angle restraint at the minimum of 170 degree is as follow: r1=0, r2=170, r3=170, r4=360, where r2=r3, and r1<<r2, r3<<r4. Similarly, the restraint at the minimum of 10 degree can be r1=-160, r2=10, r3=10, r4=200. I think the "r1=-160" here is reasonable (minus degree of angle has a physical meaning). However, if I want to impose a bond length restraint at the minimum of 1.2 angstrom, how can I choose the r1 and r4? If I use r1=0.2, r2=1.2, r3=1.2, r4=2.2, it seems that r1 and r4 do not satisfy the requirement that "r1 and r4 should far away from r2 (or r3), so that the potential is essentially harmonic everywhere". However, if I use r1=-8.8, r2=1.2, r3=1.2, r4=11.2, there still has a problem: what does the r1=-8.8 mean?

(2) For a given step size between different windows, is there any general rule to choose the force constant? In my calculations, I do some test calculations to make sure the overlapping of sampling between neighbor windows is good enough. In principle, PMF results should not depend on the force constant used in each window. However, from my test calculations, I find that different force constants may have some different PMF results after long time samplings. So I am confused about the force constant.

Many thanks for any suggestion.

Best,

Hao Dong

2010-06-02

dhacademic

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jun 02 2010 - 11:30:03 PDT

Date: Wed, 2 Jun 2010 14:17:57 -0400

Dear Amber users,

I have two questions about the restraint in umbrella sampling.

(1) According to the Amber9 tutorial (p159), the torsion angle restraint at the minimum of 170 degree is as follow: r1=0, r2=170, r3=170, r4=360, where r2=r3, and r1<<r2, r3<<r4. Similarly, the restraint at the minimum of 10 degree can be r1=-160, r2=10, r3=10, r4=200. I think the "r1=-160" here is reasonable (minus degree of angle has a physical meaning). However, if I want to impose a bond length restraint at the minimum of 1.2 angstrom, how can I choose the r1 and r4? If I use r1=0.2, r2=1.2, r3=1.2, r4=2.2, it seems that r1 and r4 do not satisfy the requirement that "r1 and r4 should far away from r2 (or r3), so that the potential is essentially harmonic everywhere". However, if I use r1=-8.8, r2=1.2, r3=1.2, r4=11.2, there still has a problem: what does the r1=-8.8 mean?

(2) For a given step size between different windows, is there any general rule to choose the force constant? In my calculations, I do some test calculations to make sure the overlapping of sampling between neighbor windows is good enough. In principle, PMF results should not depend on the force constant used in each window. However, from my test calculations, I find that different force constants may have some different PMF results after long time samplings. So I am confused about the force constant.

Many thanks for any suggestion.

Best,

Hao Dong

2010-06-02

dhacademic

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Jun 02 2010 - 11:30:03 PDT

Custom Search