Hi Berk,<div><br></div><div>I am extremely sorry, here is the correct log file</div><div><br></div><div>++++++++++++++++</div><div>grpopts:</div><div><div> nrdf: 0 0</div><div> ref_t: 300 0</div>
<div> tau_t: 0.1 0.1</div><div>++++++++++++++++</div><div><br></div><div>Thanks </div><div>Srinivas.</div><div><br></div><br><div class="gmail_quote">On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>
Ah, but that does not correspond to the mdp options tou mailed.<br>Here there is only one group with 0 degrees of freedom and reference temperature 0.<br><br>Berk<br><br><hr>Date: Fri, 26 Feb 2010 10:50:13 -0500<div><div>
</div><div class="h5"><br>Subject: Re: [gmx-users] problem with the size of freeze groups<br>From: <a href="mailto:jampanis@gmail.com" target="_blank">jampanis@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>HI<div><br></div><div>Thanks, My log file shows me "nrdf: 0"</div><div><br></div><div>###############</div><div><br></div><div><div> grpopts:</div><div> nrdf: 0</div><div> ref_t: 0</div>
<div> tau_t: 0</div><div><br></div><div>###############</div><div><br></div><div>Thanks</div><div>Srinivas.</div></div><div><br><div>On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div>
Hi,<br><br>Then I have no clue what might be wrong.<br>Have you check nrdf in the log file?<br><br>Berk<br><br><hr>Date: Fri, 26 Feb 2010 09:54:22 -0500<br>Subject: Re: [gmx-users] problem with the size of freeze groups<div>
<div></div><div><br>From: <a href="mailto:jampanis@gmail.com" target="_blank">jampanis@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br>Dear Berk,<div>
<br></div><div>Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same.</div><div>Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file?</div>
<div><br></div><div>Thanks again</div><div>Srinivas.</div><div><br></div><div>md.mdp file</div><div><br></div><div>+++++++++++++++++++++++++++++++++++++++++++++++</div><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(51, 51, 51)">title = AB2130<br>
cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 1500000 ; total 3.0 ns.<br>nstcomm = 1<br>nstxout = 1000 ; collect data every 2.0 ps<br>
nstvout = 1000 ; collect velocity every 2.0 ps<br>nstfout = 0<br>nstlog = 0<br>nstenergy = 1000 ; collect energy every 2.0 ps<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>
coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.0<br>rvdw_switch = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>
optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<br>tau_t = 0.1 0.1<br>tc-grps = Tmp1 Tmp2<br>ref_t = 300 0<br>gen_vel = yes<br>
gen_temp = 300.0<br>acc_grps = Tmp2<br>accelerate = 0.1 0.1 0.1<br>gen_seed = 173529<br>freezegrps = Tmp2<br>freezedim = Y Y Y</span></div><div>+++++++++++++++++++++++++++++++++++++++++++++++<br>
<br><div>On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br><blockquote style="padding-left:1ex">
<div>
Hi,<br><br>It seems there is a bug in grompp, which subtracts degrees of freedom for<br>constraints in water also for frozen water molecules.<br>I guess the md.log file reports zero degrees of freedom for your t-coupl group.<br>
You can circumvent this issue by putting all your frozen atoms in a separate<br>t-coupling group.<br><br>Berk<br><br><hr>Date: Wed, 24 Feb 2010 21:34:30 -0500<br>From: <a href="mailto:jampanis@gmail.com" target="_blank">jampanis@gmail.com</a><div>
<br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>Subject: [gmx-users] problem with the size of freeze groups<div><div></div><div><br><br><div>Dear Gromacs Users,</div>
<div><br>I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for MD, and temp coupling is applied for freezing and non freezing waters separately. In case of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5 cm2/s (comparable with bulk), but the system with 25 Å radius gives me almost 0 diffusion coefficient. When I open the log file of 25 Å system it shows the initial temperature as zero.</div>
<div><br>Is there any relation between size of freezing group and temperature coupling? How the sphere with 35 Å radius is working fine but not with the radius 25 Å?</div>
Can anybody help me?<br>
Here is my m.mdp file<br>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>title = AB2130<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 1500000 ; total 3.0 ns.<br>
nstcomm = 1<br>nstxout = 1000 ; collect data every 2.0 ps<br>nstvout = 1000 ; collect velocity every 2.0 ps<br>nstfout = 0<br>nstlog = 0<br>nstenergy = 1000 ; collect energy every 2.0 ps<br>
nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.0<br>rvdw_switch = 0.9<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = V-rescale<br>tau_t = 0.1 0.1<br>
tc-grps = Tmp1 Tmp2<br>ref_t = 300 0<br>gen_vel = yes<br>gen_temp = 300.0<br>acc_grps = Tmp2<br>accelerate = 0.1 0.1 0.1<br>gen_seed = 173529<br>freezegrps = Freez<br>
freezedim = Y Y Y<br>+++++++++++++++++++++++++++++++++++++++++++++++++++++++<br clear="all"><br>-- <br>*********************************************<br>J. Srinivasa Rao<br>Post-doctoral Research Associate<br>Computational Biophysics Group<br>
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