<br>Dear gromacs users,<br><br> I went through the papers <a href="http://dx.doi.org/10.1021/jp003919d" target="_blank">dx.doi.org/10.1021/jp003919d</a>. on OPLS,<br>Its is stated in the paper<br><br>"Intermolecular interactions were truncated at 11 Å, with the standard <br>
correction for the interactions beyond that radius. The electrostatic <br>interactions were quadratically feathered to zero over the last 0.5 Å <br>before the cutoff distance."<br><br><br>another OPLS reference <br>"Optimized Intermolecular Potential Functions for Liquid<br>
Hydrocarbons" - J. Am. Chem. Soc. 1984, 106, 6638-6646<br><br>"In most cases, the intermolecular nonbonded interactions were truncated<br>at 11 Å based on roughly the center-of-mass separations with quadratic<br>
smoothing of the interaction energy to zero over the last 0.5 Å. The cutoff<br>for alkenes and acetals was 13 Å, while for propanol, cyclohexane,<br>2-methyl-2-propanol, phenol, ethyl methyl sulfide, NMA, DMA, and NMP it was <br>
extended to 15 Å."<br><br>So from these and other references of OPLS - AA force field, is it possible to<br>set a range for vdw, coulomb interactions, so that we can use in that range <br>according to the system we are working on?<br>
<br>Pardon me if the question is wrong. Your references and books will be of<br>great help for me.<br><br>Can anyone suggest regarding the preference of vdw_type (cutoff/shift or <br>
switch),<br><br>Thank you <br>MKS<br><br><br><br> <br><br> <br><div class="gmail_quote">On Sat, Jan 22, 2011 at 11:18 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 class="im"><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;">
I went through few papers related to OPLS-AA, but could not find<br>
any specific values mentioned for vdw and coulomb intecations..<br>
In one of the papers<br>
".....In most cases, the intermolecular nonbonded interactions were<br>
truncated at 11Å based on roughly the center-of-mass separations<br>
with quadratic smoothing of the interaction energy to zero over the<br>
last 0.5 Å. The cutoff for alkenes and acetals was 13 Å, while for<br>
propanol, cyclohexane, 2-methyl-2-propanol, phenol, ethyl methyl<br>
sulfide, NMA, DMA, and NMP it was extended to 15 Å....."<br>
J. Am. Chem. Soc. 1996, 118, 11225-11236.<br>
<br>
</blockquote>
<br></div>
That is an older version of OPLS. See <a href="http://dx.doi.org/10.1021/jp003919d" target="_blank">dx.doi.org/10.1021/jp003919d</a>. The cutoffs are much clearer.<br><font color="#888888">
<br>
-Justin<br>
<br>
</font><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
So does this cut off refer to coulombic interactions?<br>
is it correct if iI use the following parameters for OPLS-AA force field?<br>
<br>
-----------------------------------------------------------------------------<br>
;NEIGHBOUR SEARCHING<br>
nstlist = 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 = 1.4 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST<br>
<br>
;ELECTROSTATICS<br>
coulombtype = PME ; METHOD FOR CALCULATING COULOMIC INTERCATION - PARTICLE MESH EWALD<br>
rcoulomb = 1.4 ; 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<br>
rvdw = 1.00 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS<br>
--------------------------------------------------------------------------------------------------------------------<br>
<br>
<br>
Thanks<br>
MKS<br>
<br>
<br></div><div class="im">
On Sat, Jan 22, 2011 at 6:41 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>
Kavyashree M wrote:<br>
<br>
Sir,<br>
<br>
Yes sir I am using PME. And one more thing I noticed was,<br>
the protein has<br>
7 disulphide bonds, so when I reduce all the cystine to cysteine<br>
or to alanine,<br>
the the sum of charge group radii reduces from 0.31..nm to<br>
0.30..nm and also the<br>
value of this is identical in case of alanine mutation or<br>
cysteine mutation.<br>
I finalised on the value of rlist = rcolomb = 1.35nm so as<br>
not to take risk.<br>
is that fine?<br>
<br>
<br>
As I said before, read the OPLS paper. 1.35 nm does not sound right.<br>
<br>
-Justin<br>
<br>
Thank you<br>
M. Kavyashree<br>
<br>
<br>
On Sat, Jan 22, 2011 at 6:26 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 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>
Kavyashree M wrote:<br>
<br>
Sir,<br>
<br>
System is a protein with 123 aa. No modifications<br>
were made<br>
on the pdb file,<br>
and it was submitted to pdb2gmx by removing all HETATMs,<br>
retaining only protein<br>
atoms. topology was created entirely by pdb2gmx and no other<br>
molecule was introduced.<br>
<br>
I will go through the OPLSAA paper, but if I increase<br>
rlist<br>
to 1.4nm without reducing<br>
rvdw according to "The Origin of Layer Structure Artifacts in<br>
Simulations of Liquid Water"<br>
- JCTC, 2006, 2, 1-11, will it not cause orderedwater shell<br>
during simultion?<br>
<br>
<br>
You're using PME. In the first paragraph of the<br>
introduction, it is<br>
stated that the spurious effect does not occur with PME.<br>
<br>
-Justin<br>
<br>
<br>
Thanking you<br>
M. Kavyashree<br>
<br>
<br>
On Sat, Jan 22, 2011 at 12:27 AM, 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>
<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>>><br>
<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>><br>
<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>
Kavyashree M wrote:<br>
<br>
Sir,<br>
<br>
What exactly can be wrong with the topology? As<br>
I tried<br>
with<br>
<br>
<br>
I don't know, what's in your system? Was the topology<br>
created<br>
entirely by pdb2gmx, or have you introduced some other<br>
molecules<br>
that you've parameterized?<br>
<br>
<br>
different PDBs of same structure at higher resolutions<br>
too, I am<br>
getting<br>
almost similar charge group radii, so can you kindly<br>
elaborate about<br>
what can go wrong in the topology to get such values?<br>
<br>
<br>
Large charge groups indicate that a fair number of<br>
atoms have<br>
been<br>
included in the same charge group. Usually only two<br>
or three<br>
atoms<br>
are in a charge group, rendering them fairly small. With<br>
PME, the<br>
effects may not be that large, i.e.<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html</a>,<br>
but it's still worth investigating what your largest<br>
charge<br>
group is<br>
that's causing this problem. If the topology is sound<br>
and is<br>
based<br>
entirely upon standard force field files, it may<br>
suffice to<br>
simply<br>
increase rlist to 1.4 nm, leaving all the other<br>
cutoffs at 1.0,<br>
which I believe is standard for OPLS (but don't just<br>
take my word<br>
for it).<br>
<br>
-Justin<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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>><br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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