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From: oguz gurbulak <gurbulakoguz.gmail.com>

Date: Sat, 7 Mar 2009 20:04:19 +0200

Dear Amber Users,

I'm interested in evaluating thermophysical and rheological properties of

n-alkanes and binary mixtures of n-alkanes. I performed md simulations using

Amber 10 v. and I want to do analysis with my Amber trajectory files. My

aim is to get Self Diffusion coefficents from calculating MSD and velocity

autocorrelation functions and to get shear viscosity from calculating the

autocorrelation functions of the stress tensors. For this reason, I

searched Amber manuals, tutorials and mail archives in order to have enough

information about these operations. I learned that ''diffusion'' command in

ptraj can calculates MSD and 'analyze timecorr' option of ptraj can

calculates time correlation functions. I read this part of Amber manual, but

I didn't see any procedure in order to calculate velocity autocorrelation

functions. According to me part of the problem is likely because velocities

are not output into the mdcrd files. I thought that I can do this manually

by first outputting different restart files instead of overwriting them.

Then manually extracting velocities and calculating the autocorrelations. Am

I right ? Could you please give me the right information about this

operation ? How can I calculate velocity autocorrelation functions in ptraj

?

Ptraj input files :

trajin foo.mdcrd

trajout restart restart

trajin foo.mdvel

trajout restart restart

And, in order to get shear viscosity I need to obtain the autocorrelation

functions of the stress tensors. But I didn't find any information on this

procedure. Is it right that Amber can't calculate the autocorrelation

functions of the stress tensors ? If so, I thought that if I can to get the

calculated accelerations and pressure tensor elements at the end of each

record of md simulation, I can manually calculate shear viscosity by myself.

I think Amber must have written the calculated accelerations and pressure

tensor elements at the end of each record of md simulation. But the problem

is how can I extract these informations as a output file. Ưn this point I

strongly need your help to learn much about this procedure. Is there a way

to extract these informations as a output file ?

Thanks in advance.

Sincerely

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Mar 08 2009 - 01:19:49 PST

Date: Sat, 7 Mar 2009 20:04:19 +0200

Dear Amber Users,

I'm interested in evaluating thermophysical and rheological properties of

n-alkanes and binary mixtures of n-alkanes. I performed md simulations using

Amber 10 v. and I want to do analysis with my Amber trajectory files. My

aim is to get Self Diffusion coefficents from calculating MSD and velocity

autocorrelation functions and to get shear viscosity from calculating the

autocorrelation functions of the stress tensors. For this reason, I

searched Amber manuals, tutorials and mail archives in order to have enough

information about these operations. I learned that ''diffusion'' command in

ptraj can calculates MSD and 'analyze timecorr' option of ptraj can

calculates time correlation functions. I read this part of Amber manual, but

I didn't see any procedure in order to calculate velocity autocorrelation

functions. According to me part of the problem is likely because velocities

are not output into the mdcrd files. I thought that I can do this manually

by first outputting different restart files instead of overwriting them.

Then manually extracting velocities and calculating the autocorrelations. Am

I right ? Could you please give me the right information about this

operation ? How can I calculate velocity autocorrelation functions in ptraj

?

Ptraj input files :

trajin foo.mdcrd

trajout restart restart

trajin foo.mdvel

trajout restart restart

And, in order to get shear viscosity I need to obtain the autocorrelation

functions of the stress tensors. But I didn't find any information on this

procedure. Is it right that Amber can't calculate the autocorrelation

functions of the stress tensors ? If so, I thought that if I can to get the

calculated accelerations and pressure tensor elements at the end of each

record of md simulation, I can manually calculate shear viscosity by myself.

I think Amber must have written the calculated accelerations and pressure

tensor elements at the end of each record of md simulation. But the problem

is how can I extract these informations as a output file. Ưn this point I

strongly need your help to learn much about this procedure. Is there a way

to extract these informations as a output file ?

Thanks in advance.

Sincerely

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Sun Mar 08 2009 - 01:19:49 PST

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