Hi,<br><br><i><span class="w">quote from a paper:</span><span class="st"> </span>A twin range cut-off for van der Waals (0.9/1.4 nm) and a smooth particle mesh Ewald algorithm for Coulomb interactions (switching distance of 0.9 nm) were used.</i><br>
<br>i.e.<span id="result_box" class="short_text" lang="en"><span class="hps">this means</span></span>:<br><br>; NEIGHBORSEARCHING PARAMETERS<br>..... <br>rlist = 0.9<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>
coulombtype = PME <br>rcoulomb = 0.9 <br>vdw-type = Cut-off<br>rvdw = 1.4 <br><br>Am I wrong? <br>A twin range cut-off for van der Waals (0.9/1.4 nm) means rlist/rvdw. isnt it?<i><br>
</i><br>Thanks in advance<i><br><br></i><div class="gmail_quote">22 Mart 2012 01:32 tarihinde Oliver Stueker <span dir="ltr"><<a href="mailto:ostueker@gmail.com">ostueker@gmail.com</a>></span> yazdı:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Ahmet,<br>
<div class="im"><br>
> Let's imagine a sphere(two concentric spheres):<br>
> radius of the inside small sphere=rvdw<br>
> radius of the big sphere=rcoulomb<br>
> distance between two of our nested spheres:rlist<br>
> is this approach correct?<br>
<br>
</div>No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the<br>
Gromacs Manual.<br>
The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone<br>
for the fact that the<br>
neighbor-lists are only updated every nstlist steps (often nstlist = 5).<br>
<br>
Oliver<br>
<br>
2012/3/21 ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>>:<br>
<div class="HOEnZb"><div class="h5">> Dear users,<br>
><br>
> Berk Hess says:<br>
> [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units<br>
> Mon Jul 16 14:17:12 CEST 2007<br>
><br>
> There are three options in Gromacs.<br>
><br>
> The option you want is rcoulomb < rlist and rvdw < rlist.<br>
> This works and gives the most accurate and also the most costly integration.<br>
><br>
> A faster and very commonly used setting is: rlist=rcoulomb=rvdw.<br>
> With PME the Coulomb interactions are very small at the cut-off,<br>
> as are the LJ interactions.<br>
> So with a small sacrifice in integration accuracy one can gain a lot<br>
> of performance, also because analytical LJ is cheaper than tabulated.<br>
><br>
> The last option is rcoulomb > rlist and/or rvdw > rlist.<br>
> Then the energies and forces beyond rlist are only updated every nslist<br>
> steps.<br>
> This gives less integration accuracy but can give a lot of "interaction"<br>
> accuracy<br>
> at a small computational cost.<br>
><br>
> Justin A. Lemkul says:<br>
> [gmx-users] Twin-range cut-off<br>
> Tue Sep 13 01:25:28 CEST 2011<br>
><br>
><br>
> A twin-range cutoff just means that your short-range cutoffs aren't all the<br>
> same<br>
> value, such that they form two interaction zones. Within the shortest, the<br>
> neighbor list is updated every step. Between the shortest and longest<br>
> cutoffs,<br>
> the neighbor list is updated every nstlist steps. For instance:<br>
><br>
> rlist = 0.9<br>
> rcoulomb = 0.9<br>
> rvdw = 1.4<br>
><br>
> are common settings for Gromos96 force fields (in conjunction with PME).<br>
> Thus<br>
> there are two interaction zones - the first is if two atoms (or charge<br>
> groups,<br>
> depending on the algorithm) are within 0.9 nm, and the second is if the two<br>
> interacting species are beyond 0.9 nm but within 1.4 nm of each other.<br>
><br>
> rcoulomb: distance for Coulomb cut-off (nm)<br>
> rvdw:distance for LJ or Buckingham cut-off (nm)<br>
> nstlist: neighbor list update frequency<br>
> rlist: cut-off distance of the short-range neighbor<br>
> Twin range cutoff consists of rcoulomb and rvdw, isnt it?<br>
><br>
> Let's imagine a sphere(two concentric spheres):<br>
> radius of the inside small sphere=rvdw<br>
> radius of the big sphere=rcoulomb<br>
> distance between two of our nested spheres:rlist<br>
> is this approach correct?<br>
> I could not understand the fourierspacing and rlist.<br>
><br>
><br>
> Thanks in advance<br>
><br>
><br>
><br>
> 21 Mart 2012 20:53 tarihinde ahmet yıldırım <<a href="mailto:ahmedo047@gmail.com">ahmedo047@gmail.com</a>> yazdı:<br>
><br>
>> Dear users,<br>
>><br>
>> I have two configuration as the following related to Neigborsearching,<br>
>> Electrostatics and vdw options. I checked the literature:<br>
>> Generally the rlist, rcoulomb and rvdw have used as the following.<br>
>> rlist=1<br>
>> rcoulomb=0.8<br>
>> rvdw=1.4<br>
>><br>
>> Is there much difference between the following two options in the<br>
>> calculation/the results? Is there one significant difference between the two<br>
>> options. If yes, then what is it? What is relationship between rlist,<br>
>> nstlist and rvdw/rcoulomb?<br>
>><br>
>> Furthermore,<br>
>> fourierspacing = 0.16<br>
>> or<br>
>> fourierspacing = 0.12<br>
>> difference between these two options?<br>
>><br>
>> 1.choice<br>
>> .....<br>
>> ; NEIGHBORSEARCHING PARAMETERS<br>
>> nstlist = 5<br>
>> ns-type = Grid<br>
>> pbc = xyz<br>
>> rlist = 1.0<br>
>><br>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
>> coulombtype = PME<br>
>> pme_order = 4<br>
>> fourierspacing = 0.16<br>
>> rcoulomb = 1.0<br>
>> vdw-type = Cut-off<br>
>> rvdw = 1.0<br>
>> ...<br>
>><br>
>> 2.choice<br>
>> ..<br>
>> ; NEIGHBORSEARCHING PARAMETERS<br>
>> nstlist = 5<br>
>> ns-type = Grid<br>
>> pbc = xyz<br>
>> rlist = 0.9<br>
>><br>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
>> coulombtype = PME<br>
>> pme_order = 4<br>
>> fourierspacing = 0.16<br>
>> rcoulomb = 0.9<br>
>> vdw-type = Cut-off<br>
>> rvdw = 1.4<br>
>> ...<br>
>><br>
>> Thanks in advance<br>
>> --<br>
>> Ahmet Yıldırım<br>
>><br>
><br>
><br>
><br>
> --<br>
> Ahmet Yıldırım<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br><br clear="all"><br>-- <br>Ahmet Yıldırım<br><br>