hello<div><br></div><div>Here they are the command line and mdp file. I use Gromacs 4.5.3. This is a test case only and the protein is 1UBQ. Grompp wills top for about 10 minutes then go through.</div><div><br></div><div>***********output of grompp*****************</div>
<div><br></div><div><div>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#</div><div>Generated 2278 of the 2278 non-bonded parameter combinations</div><div>Generating 1-4 interactions: fudge = 0.5</div><div>Generated 2278 of the 2278 1-4 parameter combinations</div>
<div>Excluding 3 bonded neighbours molecule type 'Protein'</div><div>turning H bonds into constraints...</div><div>Excluding 2 bonded neighbours molecule type 'SOL'</div><div>turning H bonds into constraints...</div>
<div>Coupling 1 copies of molecule type 'Protein'</div><div>Setting gen_seed to 8552</div><div>Velocities were taken from a Maxwell distribution at 300 K</div></div><div>********************************</div><div>
<br></div><div>Command line and mdp file:</div><div><br></div><div>******************************</div><div>grompp -f pr1.mdp -c after_em.gro -t em.trr -p topol.top -o pr1</div><div>******************************</div><div>
<div>define<span class="Apple-tab-span" style="white-space:pre"> </span>= -DPOSRES<span class="Apple-tab-span" style="white-space:pre"> </span>; position restrain the protein</div><div>; Run parameters</div><div>integrator<span class="Apple-tab-span" style="white-space:pre"> </span>= sd<span class="Apple-tab-span" style="white-space:pre"> </span>; leap-frog integrator</div>
<div>nsteps<span class="Apple-tab-span" style="white-space:pre"> </span>= 5000<span class="Apple-tab-span" style="white-space:pre"> </span>; 2 * 50000 = 100 ps</div><div>dt<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.002<span class="Apple-tab-span" style="white-space:pre"> </span>; 2 fs</div>
<div>; Output control</div><div>nstxout<span class="Apple-tab-span" style="white-space:pre"> </span>= 1000<span class="Apple-tab-span" style="white-space:pre"> </span>; save coordinates every 2 ps</div><div>nstvout<span class="Apple-tab-span" style="white-space:pre"> </span>= 5000<span class="Apple-tab-span" style="white-space:pre"> </span>; save velocities every 100ps </div>
<div>nstenergy<span class="Apple-tab-span" style="white-space:pre"> </span>= 1000<span class="Apple-tab-span" style="white-space:pre"> </span>; save energies every 2 ps</div><div>nstlog<span class="Apple-tab-span" style="white-space:pre"> </span>= 1000<span class="Apple-tab-span" style="white-space:pre"> </span>; update log file every 2 ps</div>
<div>; Bond parameters</div><div>continuation<span class="Apple-tab-span" style="white-space:pre"> </span>= no<span class="Apple-tab-span" style="white-space:pre"> </span>; first dynamics run</div><div>constraint_algorithm = lincs<span class="Apple-tab-span" style="white-space:pre"> </span>; holonomic constraints </div>
<div>constraints<span class="Apple-tab-span" style="white-space:pre"> </span>= hbonds<span class="Apple-tab-span" style="white-space:pre"> </span>; H bonds constrained</div><div>lincs_iter<span class="Apple-tab-span" style="white-space:pre"> </span>= 1<span class="Apple-tab-span" style="white-space:pre"> </span>; accuracy of LINCS</div>
<div>lincs_order<span class="Apple-tab-span" style="white-space:pre"> </span>= 4<span class="Apple-tab-span" style="white-space:pre"> </span>; also related to accuracy</div><div>; Neighborsearching</div><div>ns_type<span class="Apple-tab-span" style="white-space:pre"> </span>= grid<span class="Apple-tab-span" style="white-space:pre"> </span>; search neighboring grid cels</div>
<div>nstlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 10<span class="Apple-tab-span" style="white-space:pre"> </span>; 20 fs</div><div>rlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.8<span class="Apple-tab-span" style="white-space:pre"> </span>; short-range neighborlist cutoff (in nm)</div>
<div>rcoulomb<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.8<span class="Apple-tab-span" style="white-space:pre"> </span>; short-range electrostatic cutoff (in nm)</div><div>rvdw<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; short-range van der Waals cutoff (in nm)</div>
<div>; Electrostatics</div><div>coulombtype<span class="Apple-tab-span" style="white-space:pre"> </span>= PME<span class="Apple-tab-span" style="white-space:pre"> </span>; Particle Mesh Ewald for long-range electrostatics</div>
<div>pme_order<span class="Apple-tab-span" style="white-space:pre"> </span>= 4<span class="Apple-tab-span" style="white-space:pre"> </span>; cubic interpolation</div><div>fourierspacing<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.12<span class="Apple-tab-span" style="white-space:pre"> </span>; grid spacing for FFT</div>
<div>; Temperature coupling is on</div><div>tcoupl<span class="Apple-tab-span" style="white-space:pre"> </span>= V-rescale<span class="Apple-tab-span" style="white-space:pre"> </span>; modified Berendsen thermostat</div>
<div>tc-grps<span class="Apple-tab-span" style="white-space:pre"> </span>= Protein Non-Protein<span class="Apple-tab-span" style="white-space:pre"> </span>; two coupling groups - more accurate</div><div>tau_t<span class="Apple-tab-span" style="white-space:pre"> </span>= 0.1<span class="Apple-tab-span" style="white-space:pre"> </span>0.1<span class="Apple-tab-span" style="white-space:pre"> </span>; time constant, in ps</div>
<div>ref_t<span class="Apple-tab-span" style="white-space:pre"> </span>= 300 <span class="Apple-tab-span" style="white-space:pre"> </span>300<span class="Apple-tab-span" style="white-space:pre"> </span>; reference temperature, one for each group, in K</div>
<div>; Pressure coupling is off</div><div>pcoupl<span class="Apple-tab-span" style="white-space:pre"> </span>= no <span class="Apple-tab-span" style="white-space:pre"> </span>; no pressure coupling in NVT</div><div>; Periodic boundary conditions</div>
<div>pbc<span class="Apple-tab-span" style="white-space:pre"> </span>= xyz<span class="Apple-tab-span" style="white-space:pre"> </span>; 3-D PBC</div><div>; Dispersion correction</div><div>DispCorr<span class="Apple-tab-span" style="white-space:pre"> </span>= EnerPres<span class="Apple-tab-span" style="white-space:pre"> </span>; account for cut-off vdW scheme</div>
<div>; Velocity generation</div><div>gen_vel<span class="Apple-tab-span" style="white-space:pre"> </span>= yes<span class="Apple-tab-span" style="white-space:pre"> </span>; assign velocities from Maxwell distribution</div>
<div>gen_temp<span class="Apple-tab-span" style="white-space:pre"> </span>= 300<span class="Apple-tab-span" style="white-space:pre"> </span>; temperature for Maxwell distribution</div><div>gen_seed<span class="Apple-tab-span" style="white-space:pre"> </span>= -1<span class="Apple-tab-span" style="white-space:pre"> </span>; generate a random seed</div>
<div>;free energy stuff</div><div>free_energy = yes </div><div>init_lambda = 0.0</div><div>delta_lambda = 0</div><div>sc_alpha =0.5</div><div>sc-power =1.0</div>
<div>sc-sigma = 0.3 </div><div>couple-moltype = Protein </div><div>couple-lambda0 = vdw-q</div><div>couple-lambda1 = none</div><div>*******************************</div><div>
<br>
</div><div>thanks.</div><div><br></div><div>dawei</div><div><br></div><div><br></div><div><br></div><br><div class="gmail_quote">On Mon, Feb 7, 2011 at 1:05 PM, TJ Mustard <span dir="ltr"><<a href="mailto:mustardt@onid.orst.edu">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">Dawei,</p>
<p style="margin:0px"> </p>
<p style="margin:0px">I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?</p>
<p style="margin:0px"> </p>
<p style="margin:0px">Thank you,</p>
<p style="margin:0px">TJ Mustard<span> </span></p><div><div></div><div class="h5">
<div style="margin:5px 0px 5px 0px">
<br>
On February 7, 2011 at 9:31 AM Da-Wei Li <<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>> wrote:<br>
<br>
<blockquote type="cite" style="margin-left:0px;padding-left:10px;border-left:solid 1px blue">
Well. It actually isn't dead but becomes very slow for large proteins. dawei<br>
<br>
<div class="gmail_quote">
On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <span><<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hi,
<div>
I did more test and found that it depended on size of the protein. Grompp will die when number of atoms of the protein is larger than about 200. Is it possible the source code limit the size of the protein that can be decoupled?
</div>
<div>
thanks.
</div>
<div>
dawei
<div>
<div>
<br>
<br>
<div class="gmail_quote">
On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <span><<a href="mailto:lidawei@gmail.com" target="_blank">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users
<div>
I tried free energy calculation but grompp couldn't go through. It stops after
</div>
<div>
*******************
</div>
<div>
<div>
Generated 2278 of the 2278 non-bonded parameter combinations
</div>
<div>
Generating 1-4 interactions: fudge = 0.5
</div>
<div>
Generated 2278 of the 2278 1-4 parameter combinations
</div>
<div>
Excluding 3 bonded neighbours molecule type 'Protein'
</div>
<div>
turning H bonds into constraints...
</div>
<div>
Excluding 2 bonded neighbours molecule type 'SOL'
</div>
<div>
turning H bonds into constraints...
</div>
<div>
Excluding 1 bonded neighbours molecule type 'CL'
</div>
<div>
turning H bonds into constraints...
</div>
<div>
Coupling 1 copies of molecule type 'Protein'
</div>
</div>
<div>
*******************
</div>
<div>
The CPU usage is 100%.
</div>
<div>
I just add following into the mdp file:
</div>
<div>
<div>
***************
</div>
<div>
free_energy = yes
</div>
<div>
init_lambda = 0.0
</div>
<div>
delta_lambda = 0
</div>
<div>
sc_alpha =0.5
</div>
<div>
sc-power =1.0
</div>
<div>
sc-sigma = 0.3
</div>
<div>
couple-moltype = Protein
</div>
<div>
couple-lambda0 = vdw-q
</div>
<div>
couple-lambda1 = none
</div>
</div>
<div>
***************
</div>
<div>
Does anyone have some idea about this problem? thanks.
</div>
<div>
Another question is whether I can switch off "two molecules" (such as protein+ligand) in free energy calculation? I searched this list and got that 4.0.7 did support this. how about 4.5.4?
</div>
<div>
dawei
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
</div><br>
</blockquote>
</div>
<p style="margin:0px"> </p>
</div></div><font color="#888888"><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>
</font></div>
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