Sir,<br><br> What exactly can be wrong with the topology? As I tried with<br>different PDBs of same structure at higher resolutions too, I am getting <br>almost similar charge group radii, so can you kindly elaborate about <br>
what can go wrong in the topology to get such values?<br><br>Thanks<br>MKS<br><br><div class="gmail_quote">On Fri, Jan 21, 2011 at 5:20 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters<br>
are as shown below:<br>
---------------------------------------------------------------------------------------------<br>
;NEIGHBOURSEARCHING PARAMETERS<br>
nstlist = 10 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED<br>
ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE<br>
pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE<br>
rlist = 1.36 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST<br>
<br>
;ELECTROSTATICS<br>
coulombtype = PME ; METHOD FOR CALCULATING COULOMBIC INTERCATION - PME<br>
rcoulomb = 1.36 ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS<br>
epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT<br>
<br>
;VAN DER WAALS<br>
vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S FORCES<br>
rvdw_switch = 0.9 ; WHEN TO START SWITCHING LJ POTENTIAL<br>
rvdw = 1.03 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS<br>
<br>
;EWALD<br>
fourierspacing = 0.12 ; GRID SPACING FOR FFT GRID FOR PME<br>
pme_order = 4 ; INTERPOLATION ORDER FOR PME<br>
ewald_rtol = 1e-5 ; RELATIVE STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL<br>
optimize_fft = yes ; SAVES A FEW PERCENT FOR LONG SIMULATIONS<br>
-----------------------------------------------------------------------------------------------------<br>
<br>
For EM (energy minimisation) I initially had used<br>
rlist = rcolomb = 1.2; rvdw = 1.1; rvdw_switch = 1.0<br>
grompp gave the message:<br>
##################<br>
Largest charge group radii for Van der Waals: 0.160, 0.157 nm<br>
Largest charge group radii for Coulomb: 0.168, 0.167 nm<br>
<br>
NOTE 1 [file md.mdp]:<br>
The sum of the two largest charge group radii (0.317) is larger than<br>
rlist (1.20000) - rvdw (1.10000)<br>
##################<br>
So I changed the values to: rlist = rcolomb = 1.35; rvdw = 1.03; rvdw_switch = 1.0<br>
grompp message during em disappeared.<br>
<br>
During PR (position refinement), Again the message appeared for grompp<br>
##################<br>
Largest charge group radii for Van der Waals: 0.168, 0.156 nm<br>
Largest charge group radii for Coulomb: 0.168, 0.164 nm<br>
<br>
NOTE 1 [file md.mdp]:<br>
The sum of the two largest charge group radii (0.324) is larger than<br>
rlist (1.35000) - rvdw (1.03000)<br>
##################<br>
hence I changed the values to: rlist = rcolomb = 1.36; rvdw = 1.03; rvdw_switch = 1.0<br>
grompp message during pr disappeared.<br>
<br>
The same message repeated for MD<br>
###################<br>
Largest charge group radii for Van der Waals: 0.171, 0.159 nm<br>
Largest charge group radii for Coulomb: 0.171, 0.166 nm<br>
<br>
NOTE 1 [file md.mdp]:<br>
The sum of the two largest charge group radii (0.330248) is larger than<br>
rlist (1.360000) - rvdw (1.030000)<br>
###################<br>
<br>
My questions are:<br>
1. Why does the charge group radii change in this way from em to pr to MD even though I<br>
am using same parameters<br>
</blockquote>
<br></div></div>
Because EM changes coordinates, so the configurations of those charge groups probably changed.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm according to "The Origin<br>
of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC, 2006, 2, 1-11 paper?)<br>
3. What is the minimum safest rvdw distance i can take?<br>
</blockquote>
<br></div>
For #2 and #3, you should use settings that are recommended for the OPLS force field. Refer to the original literature for the force field.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
4. According to the manual, when using switch they have suggested that ".. neighbor search<br>
cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in the above case it goes<br>
more than 0.3nm?<br>
<br>
</blockquote>
<br></div>
Usually over 0.3 nm is not necessary, but it seems in your case that you have some relatively large charge groups. This may or may not indicate something is wrong with your topology.<br>
<br>
The ad hoc changes you have made to the cutoffs to make a grompp message go away are probably not suitable. Refer to the OPLS papers for proper settings.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
MKS<br>
<br>
</blockquote>
<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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