hi, all<div><br></div><div>I get another strange error. Once I turn on free energy calculation. mdrun will complain this:</div><div><br></div><div><div>Initial maximum inter charge-group distances:</div><div> two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231</div>
<div> multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13</div><div>Minimum cell size due to bonded interactions: 4.960 nm</div><div><br></div><div><br></div><div>so that domain decomposition will not work. What is a LJC pair? I did not see any problem with my system. Everything is fine if free_energy = no.</div>
<div><br></div><div>thanks.</div><div><br></div><div>dawei</div><div><br></div><div><br></div><br><div class="gmail_quote">On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li <span dir="ltr"><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">hello<div><br></div><div>My goal is to study the solvation free energy of a fixed protein and compare it with implicit model. The pr1. mdp is just a test case. Grompp always need more than 10 minutes to finish for my 76 residues protein when free_energy = yes, no matter there is PR or not, whether I switch off only vdm or switch both ele and vdm.</div>
<div><br></div><div>The memory usage is <1% on a system with 16GB memory so that memory limitation can be ruled out.</div><div><br></div><div>best,</div><div><br></div><div>dawei</div><div><div></div><div class="h5"><div>
<br></div><div><br><br><div class="gmail_quote">
On Mon, Feb 7, 2011 at 1:31 PM, TJ Mustard <span dir="ltr"><<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<p style="margin:0px">Da-Wei,</p>
<p style="margin:0px"><span><br>
</span></p>
<p style="margin:0px"><span>Do you need FEP information on the PR step? Are you going to do a MD(sd) with FEP on after the PR?</span></p>
<p style="margin:0px"><span> </span></p>
<p style="margin:0px"><span>And are you doing hydration of a protein?<br>
</span></p>
<p style="margin:0px"> </p>
<p style="margin:0px">Thank you,<span> </span></p>
<p style="margin:0px"><span>TJ Mustard<font color="#888888"><br>
</font></span></p><div><div></div><div>
<div style="margin:5px 0px 5px 0px">
On February 7, 2011 at 10:23 AM "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> Da-Wei Li wrote:<br>
> > hello<br>
> ><br>
> > Here they are the command line and mdp file. I use Gromacs 4.5.3. This<br>
> > is a test case only and the protein is 1UBQ. Grompp wills top for about<br>
> > 10 minutes then go through.<br>
> ><br>
><br>
> The efficiency of this kind of process will depend on the amount of available<br>
> memory on the system. You're asking grompp to decouple a huge amount of degrees<br>
> of freedom, which will require a lot of memory to do. It sounds like it's<br>
> working, in any case, so there's no real problem.<br>
><br>
> Whether or not simultaneously decoupling the LJ and Coulombic interactions of a<br>
> whole protein will generate a stable trajectory or sensible result is another<br>
> matter.<br>
><br>
> -Justin<br>
><br>
> > ***********output of grompp*****************<br>
> ><br>
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#<br>
> > Generated 2278 of the 2278 non-bonded parameter combinations<br>
> > Generating 1-4 interactions: fudge = 0.5<br>
> > Generated 2278 of the 2278 1-4 parameter combinations<br>
> > Excluding 3 bonded neighbours molecule type 'Protein'<br>
> > turning H bonds into constraints...<br>
> > Excluding 2 bonded neighbours molecule type 'SOL'<br>
> > turning H bonds into constraints...<br>
> > Coupling 1 copies of molecule type 'Protein'<br>
> > Setting gen_seed to 8552<br>
> > Velocities were taken from a Maxwell distribution at 300 K<br>
> > ********************************<br>
> ><br>
> > Command line and mdp file:<br>
> ><br>
> > ******************************<br>
> > grompp -f pr1.mdp -c after_em.gro -t em.trr -p topol.top -o pr1<br>
> > ******************************<br>
> > define = -DPOSRES ; position restrain the protein<br>
> > ; Run parameters<br>
> > integrator = sd ; leap-frog integrator<br>
> > nsteps = 5000 ; 2 * 50000 = 100 ps<br>
> > dt = 0.002 ; 2 fs<br>
> > ; Output control<br>
> > nstxout = 1000 ; save coordinates every 2 ps<br>
> > nstvout = 5000 ; save velocities every 100ps<br>
> > nstenergy = 1000 ; save energies every 2 ps<br>
> > nstlog = 1000 ; update log file every 2 ps<br>
> > ; Bond parameters<br>
> > continuation = no ; first dynamics run<br>
> > constraint_algorithm = lincs ; holonomic constraints<br>
> > constraints = hbonds ; H 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 cels<br>
> > nstlist = 10 ; 20 fs<br>
> > rlist = 0.8 ; short-range neighborlist cutoff (in nm)<br>
> > rcoulomb = 0.8 ; 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 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, 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>
> > ;free energy stuff<br>
> > free_energy = yes<br>
> > init_lambda = 0.0<br>
> > delta_lambda = 0<br>
> > sc_alpha =0.5<br>
> > sc-power =1.0<br>
> > sc-sigma = 0.3<br>
> > couple-moltype = Protein<br>
> > couple-lambda0 = vdw-q<br>
> > couple-lambda1 = none<br>
> > *******************************<br>
> ><br>
> > thanks.<br>
> ><br>
> > dawei<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > On Mon, Feb 7, 2011 at 1:05 PM, TJ Mustard <<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a><br>
> > <mailto:<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>>> wrote:<br>
> ><br>
> > Dawei,<br>
> ><br>
> > <br>
> ><br>
> > I have no problems with proteins in the thousands of atoms. Can you<br>
> > post your command line and mdp files?<br>
> ><br>
> > <br>
> ><br>
> > Thank you,<br>
> ><br>
> > TJ Mustard<br>
> ><br>
> ><br>
> > On February 7, 2011 at 9:31 AM Da-Wei Li <<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a><br>
> > <mailto:<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>>> wrote:<br>
> ><br>
> >> Well. It actually isn't dead but becomes very slow for large<br>
> >> proteins. dawei<br>
> >><br>
> >> On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a><br>
> >> <mailto:<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>>> wrote:<br>
> >><br>
> >> hi,<br>
> >> I did more test and found that it depended on size of the<br>
> >> protein. Grompp will die when number of atoms of the protein<br>
> >> is larger than about 200. Is it possible the source code limit<br>
> >> the size of the protein that can be decoupled?<br>
> >> thanks.<br>
> >> dawei<br>
> >><br>
> >><br>
> >> On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a><br>
> >> <mailto:<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>>> wrote:<br>
> >><br>
> >> Dear users<br>
> >> I tried free energy calculation but grompp couldn't go<br>
> >> through. It stops after<br>
> >> *******************<br>
> >> Generated 2278 of the 2278 non-bonded parameter combinations<br>
> >> Generating 1-4 interactions: fudge = 0.5<br>
> >> Generated 2278 of the 2278 1-4 parameter combinations<br>
> >> Excluding 3 bonded neighbours molecule type 'Protein'<br>
> >> turning H bonds into constraints...<br>
> >> Excluding 2 bonded neighbours molecule type 'SOL'<br>
> >> turning H bonds into constraints...<br>
> >> Excluding 1 bonded neighbours molecule type 'CL'<br>
> >> turning H bonds into constraints...<br>
> >> Coupling 1 copies of molecule type 'Protein'<br>
> >> *******************<br>
> >> The CPU usage is 100%.<br>
> >> I just add following into the mdp file:<br>
> >> ***************<br>
> >> free_energy = yes<br>
> >> init_lambda = 0.0<br>
> >> delta_lambda = 0<br>
> >> sc_alpha =0.5<br>
> >> sc-power =1.0<br>
> >> sc-sigma = 0.3<br>
> >> couple-moltype = Protein <br>
> >> couple-lambda0 = vdw-q<br>
> >> couple-lambda1 = none<br>
> >> ***************<br>
> >> Does anyone have some idea about this problem? thanks.<br>
> >> Another question is whether I can switch off "two<br>
> >> molecules" (such as protein+ligand) in free energy<br>
> >> calculation? I searched this list and got that 4.0.7 did<br>
> >> support this. how about 4.5.4?<br>
> >> dawei<br>
> >><br>
> >><br>
> > <br>
> ><br>
> > TJ Mustard<br>
> > Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a> <mailto:<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>><br>
> ><br>
> ><br>
> > --<br>
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> ><br>
> ><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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</div>
<p style="margin:0px"> </p>
<p style="font-family:monospace;white-space:nowrap;margin:5px 0px 5px 0px">TJ Mustard<br>
Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p>
</div></div></div>
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