>
> Hi again,
>
> Yes. But I thought your comment was referring to "taking the potential to
> zero." Neither the cutoff implementation nor your table was doing that at
> rcutoff, so any particle in the list got computed regardless of rcutoff.
> When you saw a zero-strength interaction, that was b
Hi,
On Tue, Jan 23, 2018 at 6:27 PM Faezeh Pousaneh wrote:
> Hi Mark,
> thanks for remarks, just one point:
>
>
> > > But what I see from resulted potential vs
> > > displacement of two molecules, is that Gromacs has taken the potential
> to
> > > zero at rlist not *''rcut-off''*. That is why fo
Hi Mark,
thanks for remarks, just one point:
> > But what I see from resulted potential vs
> > displacement of two molecules, is that Gromacs has taken the potential to
> > zero at rlist not *''rcut-off''*. That is why for rcut-off > rlist the
> > result is not correct.
> >
>
> You're seeing the
Hi,
On Tue, Jan 23, 2018 at 1:31 PM Faezeh Pousaneh wrote:
> >
> >
> >
> > > For any range of cut off it gives wrong results for rlist>rcut-off.
> > >
> > > Now I understand where the problem comes. I tried to see the
> collisions
> > of
> > > two molecules with a table (user potential).
> >
>
>
>
>
> > For any range of cut off it gives wrong results for rlist>rcut-off.
> >
> > Now I understand where the problem comes. I tried to see the collisions
> of
> > two molecules with a table (user potential).
>
>
> Over what range is your interaction defined? If the potential isn't zero by
> th
Hi,
On Mon, Jan 22, 2018 at 10:25 AM Faezeh Pousaneh
wrote:
> For any range of cut off it gives wrong results for rlist>rcut-off.
>
> Now I understand where the problem comes. I tried to see the collisions of
> two molecules with a table (user potential).
Over what range is your interaction d
For any range of cut off it gives wrong results for rlist>rcut-off.
Now I understand where the problem comes. I tried to see the collisions of
two molecules with a table (user potential). From the resulted LJ potential
between two particles I see that it takes the potential to zero at rlist,
not
Hi,
Yes, you said that before. But I asked what range it worked over, ie what
range of cutoff.
Mark
On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh wrote:
> Hi Mark,
>
> For rlist=rcut-off (max one) it works correctly, but as soon as rlist>
> rcut-off it fails and gives different energies. Which I
Hi Mark,
For rlist=rcut-off (max one) it works correctly, but as soon as rlist>
rcut-off it fails and gives different energies. Which I do not understand
why. In principle, there is nothing going on after cut-off in potentials.
Best regards
On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham
wrot
Hi,
There could be. But over what range does your table work correctly? What do
you get when you have a two particle system at various displacements?
Mark
On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh wrote:
> Dear Mark,
>
> Thank you, however, the problem occurs when 'table' is used. For
> vdWt
Dear Mark,
Thank you, however, the problem occurs when 'table' is used. For
vdWtype=not-user the energies are OK and the same for both cases, as I
mentioned. So I guess there should be something wrong in the way Gromacs
interpolates the table with cutoffs and rlist.
Best regards
Best regards
Hi,
With the group scheme, when you choose nstlist > 1 then you get a list of
all the groups that satisfy rlist, whatever it is, and continue to use that
list for the whole lifetime. If you chose rlist==rcoulomb, then rcoulomb is
never considered again, because you chose to use an unbuffered list.
Hi,
I run a simple example using Table,6,12 (for LJ) with vdW type= user. Then
group scheme should be chosen.
In results, I got different LJ energies when I set rlist=rcoulomb and
rlist>rcoulomb (which is allowed in this scheme). I see in the manual that
with group scheme that can be happen. But
Hi Mark,
I implement a pseudo hard sphere potential, (LJ form potential with powers
50, 49 instead of 12,6), wiht parameter sigma and epsilon parameters and
vdW cut-off=sigma.
I used Gromacs for this and is working properly for the first step. Do you
then have an idea how big should be rlist then?
Hi,
That depends on what model you want to implement - rlist sets the radius
within which particles/groups will be placed in the neighbour list. There's
further requirements based on the other elements of the simulation with
which it has to interact, so for user tables, the group scheme is needed,
Hi,
I have a user-potential for vdw and coulomb (PME-user). I use vdW and
columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of
rlist?
sorry, I could not find in manual.
Best regards
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/M
Thanks a lot,
Best regards
On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul wrote:
>
>
> On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin, now I understood. However, I do not have any target data
>> for my system. What do you suggest? the longer rcoulomb is safer, right?
>>
>
>
On 1/14/18 11:29 AM, Faezeh Pousaneh wrote:
Thank you Justin, now I understood. However, I do not have any target data
for my system. What do you suggest? the longer rcoulomb is safer, right?
Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
any specific value. It depen
Thank you Justin, now I understood. However, I do not have any target data
for my system. What do you suggest? the longer rcoulomb is safer, right?
Best regards
On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul wrote:
>
>
> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
>
>> Thanks Justin. But I on
On 1/14/18 10:42 AM, Faezeh Pousaneh wrote:
Thanks Justin. But I only define vdW potential form, coulomb potential form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are
rlist = 0.9 (in nm)
rcoulomb= 0.9 (in nm)
fine
Thanks Justin. But I only define vdW potential form, coulomb potential form
is as in Gromacs. So I would like to have electrostatic interactions as
other systems, so are
rlist = 0.9 (in nm)
rcoulomb= 0.9 (in nm)
fine while I am using PME?
Best regards
On Sun, Jan
On 1/14/18 6:01 AM, Faezeh Pousaneh wrote:
Hi,
I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose rlist
and rcoulomb correctly? (see below please)
I'm not sure if anyone can tell you that. You're using
Hi,
I have a system of charged hard spheres (user-potential), where the vdW
cut-off should be diameter of my molecule 0.3479. I wonder if I chose rlist
and rcoulomb correctly? (see below please)
integrator= md
dt= 0.001
nsteps= 300
;
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham
> Sent: Thursday, January 12, 2017 3:17:36 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] r
___
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Mark Abraham
Sent: Thursday, January 12, 2017 3:17:36 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] rlist, rcolumb, and rvdw
Hi,
On Wed, Jan 11, 2017 at 8:11 PM Mohsen Ramezanpour <
ramezanpour.moh...@gmail
Hi,
On Wed, Jan 11, 2017 at 8:11 PM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> I found the discussion and the links inside very useful. Thanks!
>
> I agree with was discussed above. I should not mess around with cut-offs
> :-)
>
> Regarding the main question on this post (Just fo
I found the discussion and the links inside very useful. Thanks!
I agree with was discussed above. I should not mess around with cut-offs :-)
Regarding the main question on this post (Just for curiosity):
If one wish to use 0.8-0.1 (mess around :-) ), shall we change the rlist
and rcolumb to 0.1
On 1/11/17 9:42 AM, Thomas Piggot wrote:
Well, IMHO, for a lipids only system I'd would actually change those to use
rvdw-switch = 0.8. Not only is this consistent with the original CHARMM36 lipids
publication but for DPPC/POPC (at least) produces better membrane properties in
GROMACS.
See htt
Well, IMHO, for a lipids only system I'd would actually change those to
use rvdw-switch = 0.8. Not only is this consistent with the original
CHARMM36 lipids publication but for DPPC/POPC (at least) produces better
membrane properties in GROMACS.
See https://github.com/NMRLipids/NmrLipidsCholXr
On 1/11/17 2:57 AM, Mark Abraham wrote:
Hi,
Those ancient comments pertain only to the deprecated "group" cutoff
scheme. You should look at the extensive documentation of both schemes in
the current reference manuals. Particularly vdw cutoffs are baked into the
forcefield and should not be var
Hi,
Those ancient comments pertain only to the deprecated "group" cutoff
scheme. You should look at the extensive documentation of both schemes in
the current reference manuals. Particularly vdw cutoffs are baked into the
forcefield and should not be varied without extensive testing. See
http://ww
Dear gromacs users,
Reading through mailing list I found a nice discussion on the relation
between rlist, rcolumb, and rvdw:
https://www.mail-archive.com/gmx-users@gromacs.org/msg08387.html
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058507.html
If I understood co
On 6/3/14, 12:21 PM, Urszula Uciechowska wrote:
Dear Justin,
How could I change the cut-offs to make the MD more faster in my case?
Well, there are plenty of things one can do to improve performance, but the
better question is whether or not one can maintain something physically sensible
Dear Justin,
How could I change the cut-offs to make the MD more faster in my case?
/Urszula
>
>
> On 6/3/14, 4:15 AM, Urszula Uciechowska wrote:
>> Dear Gromacs users,
>>
>> I would like to run simulations with implicit water. My protein system
>> is
>> quite big it contains 784AA. I prepared e
On 6/3/14, 4:15 AM, Urszula Uciechowska wrote:
Dear Gromacs users,
I would like to run simulations with implicit water. My protein system is
quite big it contains 784AA. I prepared eM.mdp file (see below) however I
am not sure if its ok especially the rlist what should I use there in case
of s
Dear Gromacs users,
I would like to run simulations with implicit water. My protein system is
quite big it contains 784AA. I prepared eM.mdp file (see below) however I
am not sure if its ok especially the rlist what should I use there in case
of such big system.
define = -DFLEXIB
36 matches
Mail list logo
