Thanks Justin. How about note 3?<div><br></div><div><div>The largest charge group contains 12 atoms.</div><div> Since atoms only see each other when the centers of geometry of the charge</div><div> groups they belong to are within the cut-off distance, too large charge</div>
<div> groups can lead to serious cut-off artifacts.</div><div> For efficiency and accuracy, charge group should consist of a few atoms.</div><div> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.</div>
<div><br></div><div>This note reappears no matter what the parameter file has. Does this mean I need to make changes in my top file or define charge groups?</div><div><br></div><div>Pooja</div><div><br></div><br><div class="gmail_quote">
On Sat, Jul 17, 2010 at 7:25 AM, 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>
This is the .mdp file that produces notes-3 and 4. However, the previous md file produces note-3.<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
dt = 0.002<br>
nsteps = 5000000<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
nstxout = 0 ; No output, except for last frame (coordinates)<br>
nstvout = 0 ; No output, except for last frame (velocities)<br>
nstfout = 0 ; No output, except for last frame (forces)<br>
nstlog = 500000 ; Write every step to the log<br>
nstenergy = 500000 ; Write energies at every step<br>
xtc_grps = Protein<br>
nstxtcout = 500000 ; Do not write a compressed trajectory<br>
energygrps = Protein Non-Protein ; Write energy information separately for these groups<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
nstlist = 5<br>
ns-type = Grid<br>
pbc = xyz<br>
rlist = 2.0<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = Reaction-field-zero<br>
rcoulomb = 1.8<br>
epsilon_rf = 0<br>
vdw-type = Switch<br>
rvdw = 2.0<br>
rvdw-switch = 1.6<br>
<br>
</blockquote>
<br></div></div>
Well, here's the problem. Read about proper usage of the switch function, especially the note about the size of rlist:<br>
<br>
<a href="http://manual.gromacs.org/current/online/mdp_opt.html#vdw" target="_blank">http://manual.gromacs.org/current/online/mdp_opt.html#vdw</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
; Spacing for the PME/PPPM FFT<br>
fourierspacing = 0.12<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>
; Temperature coupling<br>
tcoupl = nose-hoover<br>
tc-grps = Protein Non-Protein<br>
tau_t = 0.2 0.2<br>
ref_t = 300 300<br>
<br>
; Pressure coupling pcoupl = no<br>
<br>
; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = SHAKE<br>
shake_tol = 0.0001<br>
<br>
Pooja<br>
<br>
<br>
<br></div><div><div></div><div class="h5">
On Fri, Jul 16, 2010 at 8:51 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 trying to reproduce results from a paper which uses this<br>
cutoff. The work is on loop-folding and they use implicit<br>
solvent. I am using explicit solvent with charmm 27. Below is my<br>
mdp file. I am not sure if there is any advantage in using a<br>
large cut-off.<br>
<br>
<br>
<br>
Large cutoffs can cause artifacts. This .mdp file also does not<br>
match the error message you quoted before. If it is indeed<br>
accurate, then it looks like your .mdp file is being interpreted<br>
incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a<br>
misinterpretation, file a bugzilla. If you've simply posted the<br>
wrong file, please post the correct file, if necessary. But I'd<br>
suggest you do some homework about the effects of long cutoffs,<br>
especially if they deviate from what the force field derivation<br>
requires.<br>
<br>
-Justin<br>
<br>
; VARIOUS PREPROCESSING OPTIONS<br>
title = NVT simulation (constant number,<br>
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<br>
particles by taking them randomly from a Maxwell distribution<br>
gen_temp = 300.0 ; Temperature to generate<br>
corresponding Maxwell distribution<br>
gen_seed = 9999 ; Seed for (semi) random<br>
number generation.<br>
<br>
<br>
; OPTIONS constraints = all-bonds<br>
<br>
Pooja<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<mailto:<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<br>
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<br>
of a<br>
few atoms.<br>
For all-atom force fields use: CH3, CH2, CH, NH2, NH,<br>
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<br>
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<br>
is 1777.76<br>
Number of degrees of freedom in T-Coupling group<br>
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<br>
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<br>
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
231-9080<br>
<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>
-- 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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div><div></div><div class="h5">
<br>
<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/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
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>
<mailto:<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>
<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- Quaerendo Invenietis-Seek and you shall discover.<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> <<a href="http://vt.edu" target="_blank">http://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>
-- 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 <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
</div></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>
<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/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <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/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>