Hi Gromacs friends, I am very novice to the lipid simulation study.. My problem may be very simple, But very imp to me to know it.
I am trying to reproduced the result of article ¨Antimicrobial peptide in Action¨ Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q As per article they used two conditions, 1. Stress free ( Lateral Tension = 0) 2. Stress condition ( Lateral tension = 20 mNm/m) parameter for simulation as follow, Weakly coupled temp 323 k ( Coupling time = 0.1) Weakly coupled press ( Coupling time = 0.5 Compressibility 5 e-5 bar -1) Keep the P|| ( lateral press ) and Pz( Perpendicular press ) same P|| = Pz = 1 , Result will be stress free bilayer ( Lateral Tension = 0). For other condition of P|| = -30 Pz = 1 , result in a lateral tension of 20 mNm/m for stress free condition I made following npt.mdp ; Temperature coupling is on tcoupl = Berendsen ; More accurate thermostat tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 0.5 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 5.0e-5 5.0e-5 ; isothermal compressibility, bar^-1 And for stress condition I made the following npt.mdp ; Temperature coupling is on tcoupl = Berendsen ; More accurate thermostat tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 0.5 ; time constant, in ps ref_p = -30.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 5.0e-5 5.0e-5 ; isothermal compressibility, bar^-1 Please help to make right npt.mdp from above mention parameter. I read the Gromacs manual for 4.5.4, Section 3.4 page no 33, Surface tension coupling work with only Berendsen Press coupling. Please , would you tell me how to calculate lateral surface tension from P|| ( lateral press ) and Pz( Perpendicular press ) ??? ( Why to say P|| = -30 Pz = 1 , will give the teral tension of 20 mNm/m ???) Please give me the valuable suggestion in these regard.... Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
