Thank you Justin and Peter for your responses. I tried extending the time on the npt equilibration. It helped but not much. My final pressure after the MD run was about 1.15 bar compared to ref_p which was set to 1 bar. Peter, I will try to analyze the potential error using RMSD and Drift. <br>
<br>Thanks.<br><br><div class="gmail_quote">On Mon, Apr 11, 2011 at 4:55 PM, Fabian Casteblanco <span dir="ltr"><<a href="mailto:fabian.casteblanco@gmail.com">fabian.casteblanco@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>Hi,</div>
<div> </div>
<div>I'm still in my first few months of using Gromacs. I started by creating an *.itp and *.top file for <i>Ethanol</i> 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.</div>
<div> </div>
<div>I would really appreciate anybody's help! I'm new to this but I'm eager to keep getting better.</div>
<div> </div>
<div>Thanks.</div>
<div> </div>
<div><u>NVT SCRIPT (this works fine and takes me to 298 K)</u></div>
<div>File Edit Options Buffers Tools Help<br>title =CHARMM ETHANOL NVT equilibration<br>;define =-DPOSRES ;position restrain the protein<br>;Run parameters<br>integrator =md ;leap-frog algorithm<br>
nsteps =50000 ;2 * 50000 = 100 ps<br>dt =0.002 ;2fs<br>;Output control<br>nstxout =100 ;save coordinates every 0.2 ps<br>nstvout =100 ;save velocities every 0.2 ps<br>
nstenergy =100 ;save energies every 0.2 ps<br>nstlog =100 ;update log file every 0.2 ps<br>;Bond parameters<br>continuation =no ;first dynamics run<br>constraint_algorithm=lincs ;holonomic constraints<br>
constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind<br>lincs_iter =1 ;accuracy of LINCS<br>lincs_order =4 ;also related to accuracy<br>;Neighborhood searching<br>
ns_type =grid ;search neighboring grid cells<br>nstlist =5 ;10 fs<br>rlist =1.0 ;short-range neighborlist cutoff (in nm)<br>rcoulomb =1.0 ;short-range electrostatic cutoff (in nm)<br>
rvdw =1.0 ;short-range van der Waals cutoff (in nm)<br>;Electrostatics<br>coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\<br>;ics<br>pme_order =4 ;cubic interpolation<br>
fourierspacing =0.16 ;grid spacing for FFT<br>;Temperature coupling is on<br>tcoupl =V-rescale ;modified Berendsen thermostat<br>tc_grps =SYSTEM ;two coupling groups - more accurate<br>
tau_t =0.1 ;0.1 ;time constant, in ps<br>
ref_t =298 ;25 ;reference temperature, one for each \<br>;group, in K<br>;Pressure coupling is off<br>pcoupl =no ;no pressure coupling in NVT<br>;Periodic boundary conditions<br>
pbc =xyz ; 3-D PBC<br>;Dispersion correction<br>DispCorr =EnerPres ;account for cut-off vdW scheme<br>;Velocity generation<br>gen_vel =yes ;assign velocities from Maxwell distribution<br>
gen_temp =25 ;temperature for Maxwell distribution<br>gen_seed =-1 ;generate a random seed</div>
<div>;END</div>
<div> </div>
<div><u>NPT SCRIPT</u></div>
<div>File Edit Options Buffers Tools Help<br>title =Ethanol npt equilibration<br>;define =-DPOSRES ;position restrain the protein<br>;Run parameters<br>integrator =md ;leap-frog algorithm<br>
nsteps =50000 ;2 * 50000 = 100 ps<br>dt =0.002 ;2fs<br>;Output control<br>nstxout =100 ;save coordinates every 0.2 ps<br>nstvout =100 ;save velocities every 0.2 ps<br>
nstenergy =100 ;save energies every 0.2 ps<br>nstlog =100 ;update log file every 0.2 ps<br>;Bond parameters<br>continuation =yes ;Restarting after NVT<br>constraint_algorithm=lincs ;holonomic constraints<br>
constraints =all-bonds ;all bonds (even heavy atom-H bonds)constraind<br>lincs_iter =1 ;accuracy of LINCS<br>lincs_order =4 ;also related to accuracy<br>;Neighborhood searching<br>
ns_type =grid ;search neighboring grid cells<br>nstlist =5 ;10 fs<br>rlist =1.0 ;short-range neighborlist cutoff (in nm)<br>rcoulomb =1.0 ;short-range electrostatic cutoff (in nm)<br>
rvdw =1.0 ;short-range van der Waals cutoff (in nm)<br>;Electrostatics<br>coulombtype =PME ;Particle Mesh Ewald for long-range electrostat\<br>;ics<br>pme_order =4 ;cubic interpolation<br>
fourierspacing =0.16 ;grid spacing for FFT<br>;Temperature coupling is on<br>tcoupl =V-rescale ;modified Berendsen thermostat<br>tc-grps =SYSTEM ;two coupling groups - more accurate<br>
tau_t =0.1; 0.1 ;time constant, in ps<br>
ref_t =298; 300 ;reference temperature, one for each \<br>;group, in K<br>;Pressure coupling is on<br>pcoupl =Parrinello-Rahman ;Pressure coupling on in NPT<br>pcoupltype =isotropic ;uniform scaling of box vectors<br>
tau_p =2.0 ;time constant, in ps<br>ref_p =1.0 ;reference pressure, in bar<br>compressibility =4.5e-5 ;isothermal compressibility of h2O, 1/bar<br>;Periodic boundary conditions<br>
pbc =xyz ; 3-D PBC<br>;Dispersion correction<br>DispCorr =EnerPres ;account for cut-off vdW scheme<br>;Velocity generation<br>gen_vel =no ;Velocity generation is off<br>
;gen_temp =25 ;temperature for Maxwell distribution<br>;gen_seed =-1 ;generate a random seed</div>
<div>;END</div>
<div><br clear="all"><br>-- <br></div>
<div><b><font face="arial,helvetica,sans-serif">Best regards,</font></b></div>
<div><b></b><font face="arial,helvetica,sans-serif"> </font></div>
<div><b><font face="arial,helvetica,sans-serif" size="4">Fabian F. Casteblanco</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">Rutgers University -- </font></b></div>
<div><b><font face="arial,helvetica,sans-serif">Chemical Engineering PhD Student</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">C: +908 917 0723</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">E: </font></b><a href="mailto:fabian.casteblanco@gmail.com" target="_blank"><b><font face="arial,helvetica,sans-serif">fabian.casteblanco@gmail.com</font></b></a></div>
<br>
</blockquote></div><br><br clear="all"><br>-- <br><div><b><font face="arial,helvetica,sans-serif">Best regards,</font></b></div>
<div><b></b><font face="arial,helvetica,sans-serif"> </font></div>
<div><b><font face="arial,helvetica,sans-serif" size="4">Fabian F. Casteblanco</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">Rutgers University -- </font></b></div>
<div><b><font face="arial,helvetica,sans-serif">Chemical Engineering PhD Student</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">C: +908 917 0723</font></b></div>
<div><b><font face="arial,helvetica,sans-serif">E: </font></b><a href="mailto:fabian.casteblanco@gmail.com" target="_blank"><b><font face="arial,helvetica,sans-serif">fabian.casteblanco@gmail.com</font></b></a></div><br>