<div>hello</div>
<div> </div>
<div>1. I used almost identical comands with you. </div>
<div>2. If I set "couple-intramol = yes". My grompp will run very fast.</div>
<div> </div>
<div>From the manu, "couple-intramol = no means " all intramol (protein-protein interaction in my case) interaction are turned to predefind list while "couple-intramol = yes" means intra-protein interactions are scaled the same with protein-water interaction. Maybe this is the reason my grompp becomes very slow??</div>
<div> </div>
<div>3. If I set "couple-intramol = yes", my mdrun will go very smooth. It is also fine if I turn off free energy calculation. If I set "couple-intramol=no", it will complain "two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231". This is very strange. Atom 1013 and 1231 are not bonded at all, they are actually the most <strong>far away</strong> pair in my system. I can't understand why free energy calculation will cause this message. </div>
<div> </div>
<div> </div>
<div>best,</div>
<div> </div>
<div>dawei<br></div>
<div class="gmail_quote">On Mon, Feb 7, 2011 at 6:16 PM, TJ Mustard <span dir="ltr"><<a href="mailto:mustardt@onid.orst.edu">mustardt@onid.orst.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>
<p style="MARGIN: 0px"><span>Da-Wei,</span></p>
<p style="MARGIN: 0px"><span> </span></p>
<p style="MARGIN: 0px"><span>How do you generate your box, solvent, ions?</span></p>
<p style="MARGIN: 0px"><span> </span></p>
<p style="MARGIN: 0px"><span>I use this sequence of commands:</span></p>pdb2gmx -f protein.pdb -o protein.gro -p protein.top<br>editconf -bt cubic -f protein.gro -o protein.gro -c -d 1.5<br>genbox -cp protein.gro -cs spc216.gro -o protein_b4ion.gro -p protein.top<br>
grompp -f em.mdp -c protein_b4ion.gro -p protein.top -o protein_b4ion.tpr<br>genion -s protein_b4ion.tpr -o protein_b4em.gro -neutral -conc 0.001 -pname NA -nname CL -g protein_ion.log -p protein.top<br><br>Then I will grompp and mdrun. I seldom change these values.<br>
<br>Thank you,<br>TJ Musard
<div>
<div></div>
<div class="h5"><br><br><br>
<div style="MARGIN: 5px 0px"><br>On February 7, 2011 at 1:08 PM Da-Wei Li <<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>> wrote:<br><br>
<blockquote style="BORDER-LEFT: blue 1px solid; PADDING-LEFT: 10px; MARGIN-LEFT: 0px" type="cite">hi, all
<div>I get another strange error. Once I turn on free energy calculation. mdrun will complain this: </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>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>thanks. </div>
<div>dawei </div><br>
<div class="gmail_quote">On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li <span><<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex">hello
<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>The memory usage is <1% on a system with 16GB memory so that memory limitation can be ruled out. </div>
<div>best, </div>
<div>dawei </div>
<div>
<div>
<div><br><br>
<div class="gmail_quote">On Mon, Feb 7, 2011 at 1:31 PM, TJ Mustard <span><<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; 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<span style="COLOR: #888888"><br></span></span></p>
<div>
<div>
<div style="MARGIN: 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>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> > <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please search the archive at<br>> > <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">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" target="_blank">gmx-users-request@gromacs.org</a><br>
> > <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>> > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> ><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>> ========================================<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">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" target="_blank">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>
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> </div>
<p style="MARGIN: 0px"> </p>
<p style="MARGIN: 5px 0px; FONT-FAMILY: monospace; WHITE-SPACE: nowrap">TJ Mustard<br>Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p></div></div></div><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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</blockquote></div></div></div></div></blockquote></div></div></blockquote></div>
<p style="MARGIN: 0px"> </p>
<p style="MARGIN: 5px 0px; FONT-FAMILY: monospace; WHITE-SPACE: nowrap">TJ Mustard<br>Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p></div></div></div><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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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" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote></div><br>