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 have my own tables with VDW, bonds,
angles and
Thank you! Would you suggest just a cut-off for coulmb?
Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul 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 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 = no
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 L
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 wrote:
> 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 wrote:
>
>>
>>
>> On 9/4/13
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul 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 zero
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 zero does not omit interactions. The zero is
used to trigger infinite cutoffs.
-Justin
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 wrote:
>
>
> On 9/4/13 10:35 AM, Steven Neumann wrote:
>
>> I am not using any solvent. I mimic the presence of water by vdw
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 wrote:
>
>
> On 9/4/13 10:20 AM, Steve
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