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From: thenmalar rathinavelan <thenmalrr.yahoo.co.in>

Date: Thu, 20 Feb 2003 06:21:03 +0000 (GMT)

Dear ambers,

I have some doubts regarding the usage of Nmode. I

want to compare the free energy of formation of two

DNA systems (1437 atoms). For that, I have done

steepest descent and conjugate gradient minimiztaion

using sander_classic and I am using Nmode for

Newton-Rapson minimization. I have following doubts

regarding this:

(i) If I have carried out Newton-Rapson minimization

for the convergence of 0.0001, convergence is not

reached even after 18 hours. So, I have changed the

convergence to 0.01 and now I am able to reach the

convergence within 9 hours. If I use the convergence

of 0.01 will it affect the calculation of free-energy?

(ii) I have used nvec=200, bdwnhl=0.01 and dfpred=0.1

as given in the example file (amber 4.1). Can I use

these values? otherwise how to choose these values.

(iii) In the manual (Nmode) it is mentioned that

dielc=1 and idiel=0 should be used for r^^2 distance

dependence. But, for minimization (using

sander_classic and also for anal) I have used dielc=4

and idiel=0 for 4rij. My question is that which one

should be used for the calculations - r^^2 distance

dependence or 4rij.(I have used scee=1.2 for all the

calculations, since I am using parm98.dat force field)

(iv) I have done dynamics for 4ns. Is it sufficient

if I take the last 1.5ns (at 20ps intervals) alone for

the calculation?

(v) For the calculation of free energy I am using

MM-GBSA. In /amber6/src/mm_pbsa/SOURCS/GB.F file only

the solvent dielectric constant (eps=80) is given and

not the solute dielectric constant (=1). Where should

it be given?

Kindly, tell your suggestions regarding this.

Thank you very much.

Thenmalar

________________________________________________________________________

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Received on Thu Feb 20 2003 - 06:53:00 PST

Date: Thu, 20 Feb 2003 06:21:03 +0000 (GMT)

Dear ambers,

I have some doubts regarding the usage of Nmode. I

want to compare the free energy of formation of two

DNA systems (1437 atoms). For that, I have done

steepest descent and conjugate gradient minimiztaion

using sander_classic and I am using Nmode for

Newton-Rapson minimization. I have following doubts

regarding this:

(i) If I have carried out Newton-Rapson minimization

for the convergence of 0.0001, convergence is not

reached even after 18 hours. So, I have changed the

convergence to 0.01 and now I am able to reach the

convergence within 9 hours. If I use the convergence

of 0.01 will it affect the calculation of free-energy?

(ii) I have used nvec=200, bdwnhl=0.01 and dfpred=0.1

as given in the example file (amber 4.1). Can I use

these values? otherwise how to choose these values.

(iii) In the manual (Nmode) it is mentioned that

dielc=1 and idiel=0 should be used for r^^2 distance

dependence. But, for minimization (using

sander_classic and also for anal) I have used dielc=4

and idiel=0 for 4rij. My question is that which one

should be used for the calculations - r^^2 distance

dependence or 4rij.(I have used scee=1.2 for all the

calculations, since I am using parm98.dat force field)

(iv) I have done dynamics for 4ns. Is it sufficient

if I take the last 1.5ns (at 20ps intervals) alone for

the calculation?

(v) For the calculation of free energy I am using

MM-GBSA. In /amber6/src/mm_pbsa/SOURCS/GB.F file only

the solvent dielectric constant (eps=80) is given and

not the solute dielectric constant (=1). Where should

it be given?

Kindly, tell your suggestions regarding this.

Thank you very much.

Thenmalar

________________________________________________________________________

Missed your favourite TV serial last night? Try the new, Yahoo! TV.

visit http://in.tv.yahoo.com

Received on Thu Feb 20 2003 - 06:53:00 PST

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