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

Date: Fri, 22 Apr 2011 07:20:39 -0400

You should not use such large force constants. They give high frequency

motions, ans in then require short time steps to properly integrate.

Why not use a value of 10-100 and set larger r4? You can always use the

harmonic oscillator energy equation to estimate the amount of thermal

distortion you will get.

On Apr 22, 2011 1:13 AM, "nicholus bhattacharjee" <

nicholusbhattacharjee.gmail.com> wrote:

Dear Carlos,

Thank you for your help. I have gone through the manual

and could understand the restraint energy functions. But I am facing some

problems. First of all I have changed to ialtd=1 instead of ialtd=0 since it

gives a stiffer value (hyperbolic rather than linear) beyond r4. Now as far

I could understand We can restrain the distance by either monitoring r1->r4

values or maximizing rk2 and rk3 values. Since my restrained value is very

low of around 1.8 A there is low probability of the distance coming to lower

value during MD. So if I keep the rst.dist files like bellow

&rst

ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 0.1, r2= 0.3, r3= 1.8, r4= 2.3,

rk2=0.0, rk3=2000.0, ir6=1, ialtd=1,

&end

By either giving high rk3 value (as shown above) or by giving high r4 value

I can keep the distance constrained in the desired value of around 1.8A.

This was fine with the minimization protocol (both minimization constraining

the solute as well as the whole system). But I am unable to run the

equilibrium run with this. During equilibration (where I am inceresing the

temperature from 100K to 300K) we are unable to give very high rk3 value as

it is showing problem with SHAKE where vlimit exceed. Neither giving very

high value to r4 provides a desired result i.e. I am unable to restrain the

desired distance. I am confused what should I do next. Kindly suggest some

solution.

On Mon, Apr 18, 2011 at 9:33 AM, Carlos Simmerling <

carlos.simmerling.gmail.com> wrote:

*> I don't think you should use the script- what you were doing ...
*

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Received on Fri Apr 22 2011 - 04:30:03 PDT

Date: Fri, 22 Apr 2011 07:20:39 -0400

You should not use such large force constants. They give high frequency

motions, ans in then require short time steps to properly integrate.

Why not use a value of 10-100 and set larger r4? You can always use the

harmonic oscillator energy equation to estimate the amount of thermal

distortion you will get.

On Apr 22, 2011 1:13 AM, "nicholus bhattacharjee" <

nicholusbhattacharjee.gmail.com> wrote:

Dear Carlos,

Thank you for your help. I have gone through the manual

and could understand the restraint energy functions. But I am facing some

problems. First of all I have changed to ialtd=1 instead of ialtd=0 since it

gives a stiffer value (hyperbolic rather than linear) beyond r4. Now as far

I could understand We can restrain the distance by either monitoring r1->r4

values or maximizing rk2 and rk3 values. Since my restrained value is very

low of around 1.8 A there is low probability of the distance coming to lower

value during MD. So if I keep the rst.dist files like bellow

&rst

ixpk= 0, nxpk= 0, iat= 1735, 2946, r1= 0.1, r2= 0.3, r3= 1.8, r4= 2.3,

rk2=0.0, rk3=2000.0, ir6=1, ialtd=1,

&end

By either giving high rk3 value (as shown above) or by giving high r4 value

I can keep the distance constrained in the desired value of around 1.8A.

This was fine with the minimization protocol (both minimization constraining

the solute as well as the whole system). But I am unable to run the

equilibrium run with this. During equilibration (where I am inceresing the

temperature from 100K to 300K) we are unable to give very high rk3 value as

it is showing problem with SHAKE where vlimit exceed. Neither giving very

high value to r4 provides a desired result i.e. I am unable to restrain the

desired distance. I am confused what should I do next. Kindly suggest some

solution.

On Mon, Apr 18, 2011 at 9:33 AM, Carlos Simmerling <

carlos.simmerling.gmail.com> wrote:

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Received on Fri Apr 22 2011 - 04:30:03 PDT

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