Thank you! Would you suggest just a cut-off for coulmb?
Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:03 AM, Steven Neumann wrote:
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I
want
to use PME in my mdp:
Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:11 AM, Steven Neumann wrote:
Thank you! Would you suggest just a cut-off for coulmb?
Not a finite one. The best in vacuo settings are:
pbc =
On 9/4/13 10:20 AM, Steven Neumann wrote:
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.
Sorry, this doesn't make much sense to me. If you're using implicit solvent
(GB), then it's by definition not vacuum. I also find the same to be true
On 9/4/13 10:11 AM, Steven Neumann wrote:
Thank you! Would you suggest just a cut-off for coulmb?
Not a finite one. The best in vacuo settings are:
pbc = no
rlist = 0
rvdw = 0
rcoulomb = 0
nstlist = 0
vdwtype = cutoff
coulombtype = cutoff
-Justin
On Wed, Sep 4, 2013 at 3:09 PM, Justin
On 9/4/13 10:18 AM, Steven Neumann wrote:
Thank you. i am using my own vdw tables so need a cut off.
Then I guess you have your answer. Finite cutoffs in vacuo can lead to serious
artifacts if you're not careful. Tread lightly.
-Justin
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul
On 9/4/13 10:03 AM, Steven Neumann wrote:
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want
to use PME in my mdp:
rcoulomb = 2.0
coulombtype = PME
pme_order= 4
fourierspacing = 0.12
The cutoff needs to stay like this, I
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.
On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:44 AM, Steven Neumann wrote:
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
As I said, setting the cutoffs to
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:35 AM, Steven Neumann wrote:
I am not using any solvent. I mimic the presence of
On 9/4/13 10:35 AM, Steven Neumann wrote:
I am not using any solvent. I mimic the presence of water by vdw tabulated
potentials. I wish to see what electrostatics will change. And the coulomb
cutoff = 0 will completely remove the electrostatic, right?
No, it does the opposite. Setting all
I am not using any solvent. I mimic the presence of water by vdw tabulated
potentials. I wish to see what electrostatics will change. And the coulomb
cutoff = 0 will completely remove the electrostatic, right?
On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13
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