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<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<br />
<br />
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<br />
On February 7, 2011 at 1:08 PM Da-Wei Li <lidawei@gmail.com> wrote:<br />
<br />
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
hi, all
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I get another strange error. Once I turn on free energy calculation. mdrun will complain this:
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Initial maximum inter charge-group distances:
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    two-body bonded interactions: 4.509 nm, LJC Pairs NB, atoms 1013 1231
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  multi-body bonded interactions: 0.428 nm, Proper Dih., atoms 5 13
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Minimum cell size due to bonded interactions: 4.960 nm
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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.
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thanks.
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dawei
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<div class="gmail_quote">
On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li <span><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span> wrote:<br />
<blockquote style="margin: 0 0 0 .8ex; border-left: 1px #ccc solid; padding-left: 1ex;">
hello
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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.
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The memory usage is <1% on a system with 16GB memory so that memory limitation can be ruled out.
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best,
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dawei
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<div class="h5">
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<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="margin: 0 0 0 .8ex; border-left: 1px #ccc solid; padding-left: 1ex;">
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<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>
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<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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<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>
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</blockquote>
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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