<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">In general, NVE is tricky business, since small integration errors build up and cause energy drift in the long run. Do you see energy drift too? In my experience one needs double precision and a shorter timestep than what you employ. But that is of course system dependent.<div><br></div><div>Erik<br><div><br></div><div><br><div><div>9 maj 2012 kl. 03.17 skrev Peter C. Lai:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me?<br>
-- <br>
Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br><br><div class="gmail_quote">Thanh Binh NGUYEN <<a href="mailto:nguyentb@bii.a-star.edu.sg">nguyentb@bii.a-star.edu.sg</a>> wrote:<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<pre style="white-space: pre-wrap; word-wrap:break-word; font-family: monospace"> Dear Gromacs experts,<br>> I'm just a newbaby in Gromacs, and hence I have a lot of problem <br>> when running this program. I try to run NVE simulation of a <br>> protein. First, I run an NTP ensemble, follow by NVT and finally, <br>> NVE. In NPT and NVT, T remains as constant, however, in NVE <br>> simulation, the temperature drops gradually instead of maintain <br>> approximately constant. Could you give me any advice to solve this <br>> problem?<br>> Thank you very much.<br>> Regards,<br>> Nguyen<br>><br>> P.S: below is my mdp file for three simulations:<br>> NPT ensemble:<br>> title = DEN2pro_MD<br>> define = -DFLEXIBLE<br>> constraints = all-bonds<br>> integrator = md<br>> dt = 0.002 ; ps !<br>> nsteps = 1000000 ; total 2000 ps.<br>> nstcomm = 1<br>> nstxout = 5000 ; output
coordinates every 10 ps<br>> nstvout = 5000 ; output velocities every 10 ps<br>> nstfout = 0<br>> nstlog = 10<br>> nstenergy = 10<br>> nstlist = 10<br>> ns_type = grid<br>> rlist = 0.9<br>> coulombtype = PME<br>> rcoulomb = 0.9<br>> rvdw = 1.0<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 6<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> ; Berendsen temperature coupling is on in four groups<br>> Tcoupl = berendsen<br>> tau_t = 0.1 0.1<br>> tc_grps = protein non-protein<br>> ref_t = 300 300<br>> ; Pressure coupling is on<br>> Pcoupl = berendsen<br>> pcoupltype = isotropic<br>> tau_p = 1.0<br>> compressibility = 4.5e-5<br>> ref_p = 1.0<br>> ; Generate velocites is on at 300 K.<br>> gen_vel = yes<br>> gen_temp = 300.0<br>> gen_seed = 173529<br>><br>><
br
/>><br>> NVT ensemble<br>> title = DEN2pro_MD NVT equilibration<br>> define = -DPOSRES ; position restrain the protein and ligand<br>> ; Run parameters<br>> integrator = md ; leap-frog integrator<br>> nsteps = 100000 ; 2 * 100000 = 200 ps<br>> dt = 0.002 ; 2 fs<br>> ; Output control<br>> nstxout = 5000 ; save coordinates every 10 ps<br>> nstvout = 5000 ; save velocities every 10 ps<br>> nstenergy = 100 ; save energies every 0.2 ps<br>> nstlog = 100 ; update log file every 0.2 ps<br>> energygrps = Protein<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 <br>> bonds) constrained<br>> lincs_iter = 1 ; accuracy of LINCS<br>&
gt;
lincs_order = 4 ; also related to accuracy<br>> ; Neighborsearching<br>> ns_type = grid ; search neighboring grid cells<br>> nstlist = 5 ; 10 fs<br>> rlist = 0.9 ; short-range neighborlist cutoff (in nm)<br>> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)<br>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)<br>> ; Electrostatics<br>> coulombtype = PME ; Particle Mesh Ewald for long-range <br>> electrostatics<br>> pme_order = 4 ; cubic interpolation<br>> fourierspacing = 0.12 ; grid spacing for FFT<br>> ; Temperature coupling is on<br>> tcoupl = V-rescale ; modified Berendsen thermostat<br>> tc-grps = Protein Non-protein ; two coupling groups - more accurate<br>> tau_t = 0.1 0.1 ; time constant, in ps<br>> ref_t =
300
300 ; reference temperature, <br>> one for each 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 = 300 ; temperature for Maxwell distribution<br>> gen_seed = -1 ; generate a random seed<br>><br>><br>> NVE ensemble:<br>> title = DEN2pro_MD NVE equilibration<br>> define = -DPOSRES ; position restrain the protein and ligand<br>> ; Run parameters<br>> integrator = md-vv ; leap-frog integrator<br>> nsteps = 1000000 ; 2 * 1000000 = 2000 ps<br>> dt = 0.002 ; 2 fs<br>> ; Out
put
control<br>> nstxout = 5000 ; save coordinates every 10 ps<br>> nstvout = 5000 ; save velocities every 10 ps<br>> nstenergy = 100 ; save energies every 0.2 ps<br>> nstlog = 100 ; update log file every 0.2 ps<br>> energygrps = Protein<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 <br>> bonds) constrained<br>> lincs_iter = 1 ; accuracy of LINCS<br>> lincs_order = 4 ; also related to accuracy<br>> ; Neighborsearching<br>> ns_type = grid ; search neighboring grid cells<br>> nstlist = 5 ; 10 fs<br>> rlist = 1.6 ; short-range neighborlist cutoff (in nm)<br>> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)<br>>
rlistlong = 1.6<br>> ;treatment of van der waals interactions<br>> vdwtype = Shift<br>> rvdw = 0.95 short-range van der Waals cutoff (in nm)<br>> rvdw-switch = 0.9<br>> ; Electrostatics<br>> coulombtype = PME-Switch; Particle Mesh Ewald for long-range <br>> electrostatics<br>> pme_order = 4 ; cubic interpolation<br>> fourierspacing = 0.12 ; grid spacing for FFT<br>> ; Temperature coupling is on<br>> tcoupl = no ; no temperature coupling in NVE<br>> ; Pressure coupling is off<br>> pcoupl = no ; no pressure coupling in NVE<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 = 3
00
; temperature for Maxwell distribution<br>> gen_seed = -1 ; generate a random seed<br>><br>><br><br><br><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></pre></blockquote></div></div>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
</div>
<br></div></div></body></html>