On Sat, Jul 12, 2014 at 10:45 AM, kirtana S <skirtana4.gmail.com> wrote:
> I am running an NPT simulation at 300K using sander. The
> system consists of a surface solvated in water. Here I want to calculate
> the interfacial tension for this I need to pressure tensor values.
> In my mden file I can find the values for Px Py and Pz.
>
> L0 Nsteps time(ps) Etot EKinetic
> L1 Temp T_solute T_solv Pres_scal_solu
> L2 Pres_scal_solv BoxX BoxY BoxZ
> L3 volume pres_X pres_Y pres_Z
> L4 Pressure EKCoM_x EKCoM_y EKCoM_z
> L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
> L6 VIRIAL_tot E_pot E_vdw E_el
> L7 E_hbon E_bon E_angle E_dih
> L8 E_14vdw E_14el E_const E_pol
> L9 AV_permMoment AV_indMoment AV_totMoment Density
> dV/dlamb
> da
> L0 500 0.6875000000E+04 0.2422939764E+04 0.6935114103E+04
> L1 0.2839400349E+03 0.2839400349E+03 -.4512174339E+10 0.1000000000E+01
> L2 0.1000000000E+01 0.6260445365E+02 0.6176710458E+02 0.9123224324E+02
> L3 0.3527876271E+06 -.5163074144E+03 0.3655655459E+03 -.2363064193E+03
> L4 -.1290160959E+03 0.5348740188E+02 0.7020438687E+02 0.5993247296E+02
> L5 0.1836242617E+03 0.1364413734E+04 -.8579819743E+03 0.6599244522E+03
> L6 0.1166356212E+04 -.4512174339E+04 -.7340714267E+04 -.4402385079E+03
> L7 0.0000000000E+00 0.1709692062E+04 0.4004781596E+04 0.2480820487E+04
> L8 -.7746574404E+03 -.4989803178E+04 0.8379449097E+03 0.0000000000E+00
> L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.4545390321E+00
> 0.000
> 0000000E+00
>
> Will this be relevant if I use these values.
>
I believe so. These are the values used to implement constant surface
tension for lipid bilayer simulations. Note that one component should be
"normal" to the interface while the other two will be transverse -- you
have to determine which is which for your system. Perhaps someone a bit
more knowledgeable in this area will chime in with more helpful advice.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 11:00:02 PDT
