<div><div>Hi,</div><div><br></div><div>I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off.</div>
<div><br></div><div><br></div><div>; VARIOUS PREPROCESSING OPTIONS</div><div>title = NVT simulation (constant number, pressure and temperature)</div><div>cpp = /lib/cpp</div><div>define =-DPOSRES</div>
<div><br></div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>dt = 0.002</div><div>nsteps = 100000</div><div><br></div><div>; OUTPUT CONTROL OPTIONS</div>
<div>nstxout = 10000</div><div>nstvout = 0</div><div>nstfout = 0</div><div>nstlog = 10000</div><div>nstenergy = 10000</div><div>nstxtcout = 0</div>
<div>xtc_precision = 0</div><div>xtc-grps = System</div><div>energygrps = Protein Non-Protein</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>nstlist = 5</div>
<div>ns-type = Grid</div><div>pbc = xyz</div><div>rlist = 1.8</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>coulombtype = PME</div>
<div>fourierspacing = 0.12</div><div>rcoulomb = 1.8</div><div>epsilon_rf = 78</div><div>vdw-type = Cut-off</div><div>rvdw = 1.8</div><div><br></div>
<div>; FFT grid size, when a value is 0 fourierspacing will be used =</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div>; EWALD/PME/PPPM parameters =</div>
<div>pme_order = 4</div><div>ewald_rtol = 1e-05</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div><div><br></div><div>; Temperature coupling </div><div>Tcoupl = Berendsen</div>
<div>tc-grps = Protein Non-Protein</div><div>tau_t = 0.2 0.2</div><div>ref_t = 300 300</div><div><br></div><div>; Pressure coupling </div><div>Pcoupl = Berendsen</div>
<div>Pcoupltype = Isotropic</div><div>tau_p = 1.0</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div><br></div><div>; GENERATE VELOCITIES FOR STARTUP RUN</div>
<div>gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution</div><div>gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution</div>
<div>gen_seed = 9999 ; Seed for (semi) random number generation.</div><div><br></div><div><br></div><div>; OPTIONS </div><div>constraints = all-bonds</div></div><div><br></div><div>Pooja</div>
<div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><br><br><div class="gmail_quote">On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I am getting these notes when I run grompp:<br>
<br>
NOTE 3 [file Init/ffsb_init.top]:<br>
The largest charge group contains 12 atoms.<br>
Since atoms only see each other when the centers of geometry of the charge<br>
groups they belong to are within the cut-off distance, too large charge<br>
groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br>
<br>
initialising group options...<br>
processing index file...<br>
Analysing residue names:<br>
There are: 3484 OTHER residues<br>
There are: 67 PROTEIN residues<br>
There are: 0 DNA residues<br>
There are: 0 RNA residues<br>
Analysing Protein...<br>
Analysing Other...<br>
Making dummy/rest group for Acceleration containing 11343 elements<br>
Making dummy/rest group for Freeze containing 11343 elements<br>
Making dummy/rest group for VCM containing 11343 elements<br>
Number of degrees of freedom in T-Coupling group Protein is 1777.76<br>
Number of degrees of freedom in T-Coupling group non-Protein is 20898.23<br>
Making dummy/rest group for User1 containing 11343 elements<br>
Making dummy/rest group for User2 containing 11343 elements<br>
Making dummy/rest group for XTC containing 10450 elements<br>
Making dummy/rest group for Or. Res. Fit containing 11343 elements<br>
Making dummy/rest group for QMMM containing 11343 elements<br>
T-Coupling has 2 element(s): Protein non-Protein<br>
Energy Mon. has 2 element(s): Protein non-Protein<br>
Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>
User1 has 1 element(s): rest<br>
User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>
XTC has 2 element(s): Protein rest<br>
Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>
Checking consistency between energy and charge groups...<br>
Largest charge group radii for Van der Waals: 0.288, 0.263 nm<br>
Largest charge group radii for Coulomb: 0.288, 0.263 nm<br>
<br>
NOTE 4 [file nvtp.mdp]:<br>
The sum of the two largest charge group radii (0.551009) is larger than<br>
rlist (2.000000) - rvdw (2.000000)<br>
<br>
Can someone tell me how to correct these?<br>
<br>
</blockquote>
<br></div></div>
Note 3 is explained in detail in the error message. Beyond that, read about the group concept in the manual.<br>
<br>
I've never seen Note 4 before, but a 2-nm cutoff is a bit strange for a protein simulation. Any reason you're using such large cutoffs? You may also want to provide your whole .mdp file to see if anyone can spot the underlying issue.<br>
<br>
-Justin<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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