<div>Hi,</div><div><br></div><div>This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3.</div><div><br></div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div>
<div>dt = 0.002</div><div>nsteps = 5000000</div><div><br></div><div>; OUTPUT CONTROL OPTIONS</div><div>nstxout = 0 ; No output, except for last frame (coordinates)</div>
<div>nstvout = 0 ; No output, except for last frame (velocities)</div><div>nstfout = 0 ; No output, except for last frame (forces)</div><div>nstlog = 500000 ; Write every step to the log</div>
<div>nstenergy = 500000 ; Write energies at every step</div><div>xtc_grps = Protein</div><div>nstxtcout = 500000 ; Do not write a compressed trajectory</div>
<div>energygrps = Protein Non-Protein ; Write energy information separately for these groups</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>nstlist = 5</div><div>ns-type = Grid</div>
<div>pbc = xyz</div><div>rlist = 2.0</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>coulombtype = Reaction-field-zero</div><div>rcoulomb = 1.8</div>
<div>epsilon_rf = 0</div><div>vdw-type = Switch</div><div>rvdw = 2.0</div><div>rvdw-switch = 1.6</div><div><br></div><div>; Spacing for the PME/PPPM FFT</div>
<div>fourierspacing = 0.12</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>; Temperature coupling</div>
<div>tcoupl = nose-hoover</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><div>; Pressure coupling </div><div>pcoupl = no</div><div><br></div><div>; OPTIONS FOR BONDS </div><div>constraints = all-bonds </div><div>constraint-algorithm = SHAKE</div><div>
shake_tol = 0.0001</div></div><div><br></div><div>Pooja</div><div><br></div><div><br></div><br><div class="gmail_quote">On Fri, Jul 16, 2010 at 8:51 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;"><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><div class="im">
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.<br>
<br>
<br>
</div></blockquote>
<br>
Large cutoffs can cause artifacts. This .mdp file also does not match the error message you quoted before. If it is indeed accurate, then it looks like your .mdp file is being interpreted incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a misinterpretation, file a bugzilla. If you've simply posted the wrong file, please post the correct file, if necessary. But I'd suggest you do some homework about the effects of long cutoffs, especially if they deviate from what the force field derivation requires.<br>
<br>
-Justin<br>
<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">
; VARIOUS PREPROCESSING OPTIONS<br>
title = NVT simulation (constant number, pressure and temperature)<br>
cpp = /lib/cpp<br>
define =-DPOSRES<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
dt = 0.002<br>
nsteps = 100000<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout = 10000<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 10000<br>
nstenergy = 10000<br>
nstxtcout = 0<br>
xtc_precision = 0<br>
xtc-grps = System<br>
energygrps = Protein Non-Protein<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 5<br>
ns-type = Grid<br>
pbc = xyz<br>
rlist = 1.8<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = PME<br>
fourierspacing = 0.12<br>
rcoulomb = 1.8<br>
epsilon_rf = 78<br>
vdw-type = Cut-off<br>
rvdw = 1.8<br>
<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters =<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
<br>
; Temperature coupling Tcoupl = Berendsen<br>
tc-grps = Protein Non-Protein<br>
tau_t = 0.2 0.2<br>
ref_t = 300 300<br>
<br>
; Pressure coupling Pcoupl = Berendsen<br>
Pcoupltype = Isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution<br>
gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution<br>
gen_seed = 9999 ; Seed for (semi) random number generation.<br>
<br>
<br>
; OPTIONS constraints = all-bonds<br>
<br>
Pooja<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br></div></div><div><div></div><div class="h5">
On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Sai Pooja wrote:<br>
<br>
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<br>
the charge<br>
groups they belong to are within the cut-off distance, too<br>
large charge<br>
groups can lead to serious cut-off artifacts.<br>
For efficiency and accuracy, charge group should consist of a<br>
few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,<br>
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<br>
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<br>
larger than<br>
rlist (2.000000) - rvdw (2.000000)<br>
<br>
Can someone tell me how to correct these?<br>
<br>
<br>
Note 3 is explained in detail in the error message. Beyond that,<br>
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<br>
for a protein simulation. Any reason you're using such large<br>
cutoffs? You may also want to provide your whole .mdp file to see<br>
if anyone can spot the underlying issue.<br>
<br>
-Justin<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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></blockquote><div><div></div><div class="h5">
<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>
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