Hi, I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for *Ethanol* using CHARMM force field parameters. I made the molecule and it looked fine, put 1000 molecules in a box, energy minimized it to a negative potential energy, viewed it on VMD, again looks fine. When I started running the NVT script, I set it equal to a ref_T of 298 K. It equilibrated at the temperature. Then I tried using an NPT script to equilibrate it to a ref_p of 1 bar. This is where I get the problem. The output shows the density is close to the actual experimental value of 0.789 g/cm^3. But for some reason, my pressure never gets an average of 1 bar. It keeps oscillating, which I understand is normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002). I don't understand why the ref_p of 1 bar is not working when I run this NPT.mdp script file. My simple goal is to have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and somewhere near the experimental density.
I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better. Thanks. *NVT SCRIPT (this works fine and takes me to 298 K)* File Edit Options Buffers Tools Help title =CHARMM ETHANOL NVT equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =50000 ;2 * 50000 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100 ;save coordinates every 0.2 ps nstvout =100 ;save velocities every 0.2 ps nstenergy =100 ;save energies every 0.2 ps nstlog =100 ;update log file every 0.2 ps ;Bond parameters continuation =no ;first dynamics run constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0 ;short-range neighborlist cutoff (in nm) rcoulomb =1.0 ;short-range electrostatic cutoff (in nm) rvdw =1.0 ;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc_grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1 ;0.1 ;time constant, in ps ref_t =298 ;25 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is off pcoupl =no ;no pressure coupling in NVT ;Periodic boundary conditions pbc =xyz ; 3-D PBC ;Dispersion correction DispCorr =EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =yes ;assign velocities from Maxwell distribution gen_temp =25 ;temperature for Maxwell distribution gen_seed =-1 ;generate a random seed ;END *NPT SCRIPT* File Edit Options Buffers Tools Help title =Ethanol npt equilibration ;define =-DPOSRES ;position restrain the protein ;Run parameters integrator =md ;leap-frog algorithm nsteps =50000 ;2 * 50000 = 100 ps dt =0.002 ;2fs ;Output control nstxout =100 ;save coordinates every 0.2 ps nstvout =100 ;save velocities every 0.2 ps nstenergy =100 ;save energies every 0.2 ps nstlog =100 ;update log file every 0.2 ps ;Bond parameters continuation =yes ;Restarting after NVT constraint_algorithm=lincs ;holonomic constraints constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind lincs_iter =1 ;accuracy of LINCS lincs_order =4 ;also related to accuracy ;Neighborhood searching ns_type =grid ;search neighboring grid cells nstlist =5 ;10 fs rlist =1.0 ;short-range neighborlist cutoff (in nm) rcoulomb =1.0 ;short-range electrostatic cutoff (in nm) rvdw =1.0 ;short-range van der Waals cutoff (in nm) ;Electrostatics coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\ ;ics pme_order =4 ;cubic interpolation fourierspacing =0.16 ;grid spacing for FFT ;Temperature coupling is on tcoupl =V-rescale ;modified Berendsen thermostat tc-grps =SYSTEM ;two coupling groups - more accurate tau_t =0.1; 0.1 ;time constant, in ps ref_t =298; 300 ;reference temperature, one for each \ ;group, in K ;Pressure coupling is on pcoupl =Parrinello-Rahman ;Pressure coupling on in NPT pcoupltype =isotropic ;uniform scaling of box vectors tau_p =2.0 ;time constant, in ps ref_p =1.0 ;reference pressure, in bar compressibility =4.5e-5 ;isothermal compressibility of h2O, 1/bar ;Periodic boundary conditions pbc =xyz ; 3-D PBC ;Dispersion correction DispCorr =EnerPres ;account for cut-off vdW scheme ;Velocity generation gen_vel =no ;Velocity generation is off ;gen_temp =25 ;temperature for Maxwell distribution ;gen_seed =-1 ;generate a random seed ;END -- *Best regards,* ** *Fabian F. Casteblanco* *Rutgers University -- * *Chemical Engineering PhD Student* *C: +908 917 0723* *E: **[email protected]* <[email protected]>
ethanol.itp
Description: Binary data
ethanol.top
Description: Binary data
em.gro
Description: Binary data
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