[gmx-users] gmx trjconv does not produce exact .gro file (slightly different box length)

[Faezeh Pousaneh]

Hi,

I notice that gmx trjconv  does not produce the exact .gro file (slightly
different box lengths).
I mean when i run following command

gmx trjconv  -f NPT.trr  -s NPT.tpr   -o f.gro   -pbc  mol -b 2000

I get slightly different box length than when I run gmx energy ... and
select box-X,Y,Z.

 Anyone knows why?
(I should add that I have tried looking at different frames and different
choices in -pbc flag, but still see the problem )
Best regards
---
Faezeh Pousaneh
Postdoc researcher
Department of Mechanical and Industrial Engineering
Room 219, Gløshaugen, Richard birkelands vei 2b
NTNU, Trondheim, Norway

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[gmx-users] structure

[Faezeh Pousaneh]

Hi,

I have a mixture of two component system. I want to investigate the final
structure, mainly the angles and orientations between different molecules
and atom. Anyone has idea how to do that?

thanks.

Best regards
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Re: [gmx-users] rdf at contact

[Faezeh Pousaneh]

I will be grateful if some one can reply my question,


Best regards


On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh 
wrote:

> Hi,
>
> I have a system of similar molecules, I would like to obtain the rdf at
> contact (meaning, at surface of one particle).
> What I try is; I make an index file containing only central atoms of all
> molecules, then I run:
>
>
> gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0
>  -b   14000
>
> ref 0 is a single atom
> ref 1 is rest of atoms
>
>
> Then, I find the rdf value at r=contact (radius of a molecule) from
> rdf.xvg file.
> My problem is I get very different values  for different time intervals
> (after equilibrium) . Why is that so?
>
> I appreciate if sb can help.
> Best regards
>
>
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[gmx-users] rdf at contact

[Faezeh Pousaneh]

Hi,

I have a system of similar molecules, I would like to obtain the rdf at
contact (meaning, at surface of one particle).
What I try is; I make an index file containing only central atoms of all
molecules, then I run:


gmx rdf  -f  NPT.xtc  -s  NPT.tpr  -n  index.ndx -pbc   -ref 1 -sel 0   -b
 14000

ref 0 is a single atom
ref 1 is rest of atoms


Then, I find the rdf value at r=contact (radius of a molecule) from rdf.xvg
file.
My problem is I get very different values  for different time intervals
(after equilibrium) . Why is that so?

I appreciate if sb can help.
Best regards
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Re: [gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Dear Justin

One more question please,
Do we need to have constraint in this model of CO2?  Isn't it so that we
have fixed the bond lengths and angles (180) in the topology by this method?

I run 2 simulations, one with constraints = all-angles  and the other
with constraints
= all-bonds, I get different results from them. Why?



Best regards


On Wed, Mar 7, 2018 at 2:54 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Thank you.
>
>
> Best regards
>
>
> On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
>>
>>> Dear Justin,
>>>
>>> I have 2 questions regarding your tutorial on Carbon Dioxide in this
>>> link:
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/vsites/index.html
>>>
>>> 1- I see that in your simple simulation you use no boundary conditions,
>>> pbc=no, should it be always so for this model?
>>>
>>> 2- You use
>>>   comm-mode = angular,
>>> is that necessary?
>>>
>>
>> The simulation is a simple gas-phase system, which does not use PBC and
>> hence requires angular COM motion removal.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
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>>
>
>
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[gmx-users] thermostat and barostat

[Faezeh Pousaneh]

Hi,

I simulate a system which is very sensitive to chosen thermostat and
barostat. I see information in
Gromacs webpage (*http://www.gromacs.org/Documentation/Terminology/Thermostats
*) that some
thermostat are not good for systems with very few degrees of freedom (as my
system).
Is it the same with barostats? if so, which barostat I should choose (for
no-interacting system)?

Best regards
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Re: [gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Thank you.


Best regards


On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
>
>> Dear Justin,
>>
>> I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/vsites/index.html
>>
>> 1- I see that in your simple simulation you use no boundary conditions,
>> pbc=no, should it be always so for this model?
>>
>> 2- You use
>>   comm-mode = angular,
>> is that necessary?
>>
>
> The simulation is a simple gas-phase system, which does not use PBC and
> hence requires angular COM motion removal.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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[gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Dear Justin,

I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html

1- I see that in your simple simulation you use no boundary conditions,
pbc=no, should it be always so for this model?

2- You use
 comm-mode = angular,
is that necessary?

thanks for answer.

Best regards
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[gmx-users] shear viscosity

[Faezeh Pousaneh]

Hi

I want to obtain shear viscosity for ionic mixtures. I use the method Berk
Hess gives in his paper, (J. Chem. Phy *116*, 209 (2002)).

I would like to know if this is a better method, or the
muller-plathe method (Phy. rev. E *59*, 5 (1999))?

Best regards
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Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

>
> 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 because the particles
> weren't being put in the list, and not because it was in the list and
> evaluated as zero strength.
>
> Mark, I thinks there has been misunderstanding. I never saw zero
interactions.

What I mean is: with a LJ table 6,12 given in Gromacs page (even my own
other user tables), when I take rlist=0.6 and rvdw=0.5 in .mdp file, the
resulted potential from simulation shows that instead of potential becomes
zero at rvdW=0.5, it gets zero at rlist=0.6. So many unwanted interactions
are counted.   Which is an important point to know about Gromacs fails
here.

It is OK as long as rvdw-off=rcoulmb=rlist. But if we have a case with
rvdW<rcoulomb, it fails. That is why, in order to avoid that I should
change the table manually to insert rvdW smoothly to zero.

> Mark
>
> > So the solution for me now is to put the potential in the table file to
> > > > zero manually for x>cut-off.
> > >
> > >
> > > Glancing at the kernels that implement user tables, that's what you
> > should
> > > do. That means the forces are strange and you would wish to consider a
> > form
> > > where the potential smoothly reaches zero at the cutoff.
> > >
> > > But it is better to solve the problem in
> > > > Gromacs.
> > > >
> > >
> > > It looks like the group scheme with user tables doesn't have support
> for
> > > buffered lists with a correct cutoff. That correct cutoff is only
> > available
> > > in the group scheme for potentials that do go to zero. Likely we
> > concluded
> > > that because you have the ability to express your wishes entirely in
> your
> > > table, you should do so. Or use rlist == rvdw == rcoulomb.
> > >
> > > Mark
> > >
> > > > Mark
> > > > >
> > > > >
> > > > > >
> > > > > >
> > > > > > Best regards
> > > > > >
> > > > > >
> > > > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <
> > > > mark.j.abra...@gmail.com
> > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > 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 <
> fpoosa...@gmail.com
> > >
> > > > > 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 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 <
> > > > > > mark.j.abra...@gmail.com>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > 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, 2

Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

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 consequence of the particles at displacement > rlist not
> being put into the list, so not making a contribution.
>

no, I see the particles between rcut-off and rlist  which should have no
contribution to the potential (since potential should be zero after cut-off
and rlist is bigger than rcutoff) *have* contributions, and that is what
makes the wrong results.


>
> So the solution for me now is to put the potential in the table file to
> > zero manually for x>cut-off.
>
>
> Glancing at the kernels that implement user tables, that's what you should
> do. That means the forces are strange and you would wish to consider a form
> where the potential smoothly reaches zero at the cutoff.
>
> But it is better to solve the problem in
> > Gromacs.
> >
>
> It looks like the group scheme with user tables doesn't have support for
> buffered lists with a correct cutoff. That correct cutoff is only available
> in the group scheme for potentials that do go to zero. Likely we concluded
> that because you have the ability to express your wishes entirely in your
> table, you should do so. Or use rlist == rvdw == rcoulomb.
>
> Mark
>
> > Mark
> > >
> > >
> > > >
> > > >
> > > > Best regards
> > > >
> > > >
> > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > 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 <fpoosa...@gmail.com>
> > > 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 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 <
> > > > mark.j.abra...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > 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 <
> fpoosa...@gmail.com
> > >
> > > > > wrote:
> > > > > > >
> > > > > > > > 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
> > > > > > > >
> > > > > > > >
> > > > > > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <
> > > > > > mark.j.abra...@gmail.com>
> > > > > >

Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

>
>
>
> > 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
> the time you get to the relevant cutoff, then you will produce artefacts.
>
>
> I use same 6,12 table  in Gromacs top folder, which goes to 1+rc.



> > From the resulted LJ potential
> > between two particles I see that it takes the potential to zero at rlist,
> > not at rcut-off.
> > how to deal with it now?
> >
>
> If the interaction isn't in the list, it doesn't get computed.
>

>
I hope you got my point. I assume when I define rcut-off in .mdp file, the
resulted potential should be zero after this value, so the larger rlist >
rcut-off wont make difference. 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.

So the solution for me now is to put the potential in the table file to
zero manually for x>cut-off. But it is better to solve the problem in
Gromacs.

> Mark
>
>
> >
> >
> > Best regards
> >
> >
> > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > > 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 <fpoosa...@gmail.com>
> 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 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 <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > 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 <fpoosa...@gmail.com>
> > > wrote:
> > > > >
> > > > > > 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
> > > > > >
> > > > > >
> > > > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <
> > > > mark.j.abra...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > 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.
> > > > > But
> > > > > > > with rlist > rcoulomb, you chose the list to have interactions
> > that
> > > > are
> > > > > > not
> > > > > > > within rcoulomb, so every interaction is checked at every ste

Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

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 at rcut-off.
how to deal with it now?


Best regards


On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> 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 <fpoosa...@gmail.com> 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 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 <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > 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 <fpoosa...@gmail.com>
> wrote:
> > >
> > > > 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
> > > >
> > > >
> > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > 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.
> > > But
> > > > > with rlist > rcoulomb, you chose the list to have interactions that
> > are
> > > > not
> > > > > within rcoulomb, so every interaction is checked at every step for
> > > > whether
> > > > > it is within rcoulomb, before including it. That's slower to run,
> > but a
> > > > > better approach. And of course you can't expect them to compute the
> > > same
> > > > > numbers, particularly if things move fast relative to the buffer
> size
> > > and
> > > > > list lifetime.
> > > > >
> > > > > The Verlet scheme defaults do a good job of automating all this,
> but
> > as
> > > > you
> > > > > know, there's not yet support for tabulated interactions.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosa...@gmail.com>
> > > wrote:
> > > > >
> > > > > > 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 I do not find how to
> get
> > > rid
> > > > of
> > > > > > the differences in energies? or which rlist is the case.
> > > > > >
> > > > > > However, when I run with vdW type= cutoff for both rlist
> > > > rlist=rcoulomb
> > > > > > and rlist>rcoulomb with group scheme I get similar results.
> > > > &

Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

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 <mark.j.abra...@gmail.com>
wrote:

> 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 <fpoosa...@gmail.com> wrote:
>
> > 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
> >
> >
> > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > 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.
> But
> > > with rlist > rcoulomb, you chose the list to have interactions that are
> > not
> > > within rcoulomb, so every interaction is checked at every step for
> > whether
> > > it is within rcoulomb, before including it. That's slower to run, but a
> > > better approach. And of course you can't expect them to compute the
> same
> > > numbers, particularly if things move fast relative to the buffer size
> and
> > > list lifetime.
> > >
> > > The Verlet scheme defaults do a good job of automating all this, but as
> > you
> > > know, there's not yet support for tabulated interactions.
> > >
> > > Mark
> > >
> > > On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
> > >
> > > > 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 I do not find how to get
> rid
> > of
> > > > the differences in energies? or which rlist is the case.
> > > >
> > > > However, when I run with vdW type= cutoff for both rlist
> > rlist=rcoulomb
> > > > and rlist>rcoulomb with group scheme I get similar results.
> > > >
> > > > Best regards
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

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


On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> 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. But
> with rlist > rcoulomb, you chose the list to have interactions that are not
> within rcoulomb, so every interaction is checked at every step for whether
> it is within rcoulomb, before including it. That's slower to run, but a
> better approach. And of course you can't expect them to compute the same
> numbers, particularly if things move fast relative to the buffer size and
> list lifetime.
>
> The Verlet scheme defaults do a good job of automating all this, but as you
> know, there's not yet support for tabulated interactions.
>
> Mark
>
> On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosa...@gmail.com> wrote:
>
> > 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 I do not find how to get rid of
> > the differences in energies? or which rlist is the case.
> >
> > However, when I run with vdW type= cutoff for both rlist  rlist=rcoulomb
> > and rlist>rcoulomb with group scheme I get similar results.
> >
> > Best regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] rlist- group scheme

[Faezeh Pousaneh]

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 I do not find how to get rid of
the differences in energies? or which rlist is the case.

However, when I run with vdW type= cutoff for both rlist  rlist=rcoulomb
and rlist>rcoulomb with group scheme I get similar results.

Best regards
-- 
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Re: [gmx-users] rlist

[Faezeh Pousaneh]

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?


Best regards


On Tue, Jan 16, 2018 at 12:51 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> 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,
> which means you won't have both an efficient simulation and a buffered
> list.
>
> If you're still trying to implement hard spheres with GROMACS, then as (I
> think) I've said before, you should consider alternative software (not that
> I have any insight about what might work better).
>
> Mark
>
> On Mon, Jan 15, 2018 at 11:26 AM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > 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/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] rlist

[Faezeh Pousaneh]

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
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Re: [gmx-users] rlist

[Faezeh Pousaneh]

Thanks a lot,


Best regards


On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul <jalem...@vt.edu> 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?
>>
>
> Not necessarily. Longer cutoffs do not imply greater accuracy, nor does
> any specific value. It depends on your model. You have to demonstrate to a
> skeptical audience that your methods are sound. That requires describing a
> known system and its structure, energetics, and dynamics. Then you can move
> to predicting unknowns. Without that, there's no control to determine if
> your work is meaningful or a random number generator.
>
>
> -Justin
>
>
>> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> 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 while I am using PME?
>>>>
>>>> Again, there is no standard value here and it is dictated by the
>>> functional form being used. You have a custom interaction potential, even
>>> if you're using normal PME alongside you have user-defined, tabulated vdW
>>> interactions. Presumably there should be some evaluation of what cutoffs
>>> are used to satisfy whatever the assumptions are in the parametrization
>>> of
>>> your model, i.e. you need to have some target data of a known system that
>>> tells you that your physical model (cutoffs and functional form) is
>>> right,
>>> and then you use those same settings in whatever systems are of interest.
>>>
>>> -Justin
>>>
>>>
>>> Best regards
>>>
>>>>
>>>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>
>>>>
>>>> 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 custom
>>>>>>
>>>>> potentials,
>>>>> so setting cutoffs is part of the parametrization of that potential
>>>>> itself.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> integrator= md
>>>>>
>>>>> dt= 0.001
>>>>>> nsteps= 3000
>>>>>> nstxout   = 10   ; save coordinates
>>>>>> every 0
>>>>>> ps
>>>>>> nstvout   = 10   ; save velocities
>>>>>> every
>>>>>> 0
>>>>>> ps
>>>>>> nstlog= 10   ; update log file
>>>>>> every
>>>>>> nstenergy = 10; save energies every
>>>>>> nstxtcout = 10   ; Output frequency for
>>>>>> xtc
>>>>>> file
>>>>>> xtc-precision = 10   ; precision for xtc file
>>>>>> ns_type   = grid; search neighboring grid
>>>>>> cells
>>>>>> nstlist   = 10   ;  fs
>>>>>> pbc   = xyz ; 3-D PBC
>>>>>> rlist  = 0.9 ; short-range
>>>>>> neighbor-list
>>>>>> cutoff (in nm)
>>>>>> rcoulomb  = 0.9 ; short-range
>>>>>> electrostatic
>>>>>> cutoff
>>>>>> (in nm)
>>>>>> rvdw  = 0.3479  ; short-ra

Re: [gmx-users] rlist

[Faezeh Pousaneh]

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 <jalem...@vt.edu> wrote:

>
>
> 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 while I am using PME?
>>
>
> Again, there is no standard value here and it is dictated by the
> functional form being used. You have a custom interaction potential, even
> if you're using normal PME alongside you have user-defined, tabulated vdW
> interactions. Presumably there should be some evaluation of what cutoffs
> are used to satisfy whatever the assumptions are in the parametrization of
> your model, i.e. you need to have some target data of a known system that
> tells you that your physical model (cutoffs and functional form) is right,
> and then you use those same settings in whatever systems are of interest.
>
> -Justin
>
>
> Best regards
>>
>>
>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> 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 custom
>>> potentials,
>>> so setting cutoffs is part of the parametrization of that potential
>>> itself.
>>>
>>> -Justin
>>>
>>>
>>> integrator= md
>>>
>>>>dt= 0.001
>>>>nsteps= 3000
>>>>nstxout   = 10   ; save coordinates
>>>> every 0
>>>> ps
>>>>nstvout   = 10   ; save velocities every
>>>> 0
>>>> ps
>>>>nstlog= 10   ; update log file every
>>>>nstenergy = 10; save energies every
>>>>nstxtcout = 10   ; Output frequency for xtc
>>>> file
>>>>xtc-precision = 10   ; precision for xtc file
>>>>ns_type   = grid; search neighboring grid
>>>> cells
>>>>nstlist   = 10   ;  fs
>>>>pbc   = xyz ; 3-D PBC
>>>>rlist  = 0.9 ; short-range
>>>> neighbor-list
>>>> cutoff (in nm)
>>>>rcoulomb  = 0.9 ; short-range electrostatic
>>>> cutoff
>>>> (in nm)
>>>>rvdw  = 0.3479  ; short-range van der Waals
>>>> cutoff
>>>> (in nm)
>>>>coulombtype   = PME-user ; Particle Mesh Ewald
>>>> for
>>>> long-range electrostatics
>>>>pme_order = 4   ; cubic interpolation
>>>>fourierspacing= 0.16; grid spacing for FFT
>>>>vdw-type  = user
>>>>Tcoupl= berendsen   ; modified Berendsen
>>>> thermostat
>>>>tc-grps   = co2   rest   ; two coupling
>>>> groups -
>>>> more accurate
>>>>tau_t =  0.1   0.1 ; time constant, in ps
>>>>ref_t =  179.8  179.8 ; reference temperature,
>>>> one
>>>> for
>>>> each group, in K
>>>>;tc-grps  = system
>>>> cutoff-scheme  =group
>>>>energygrps= co2 rest
>>>>Pcoupl=  berendsen ;Parrinello-Rahman
>>>>Pcoupltype= Isotropic
>>>>tau_p = 1.0
>>>>compressibility   = 6.2e-5
>>>>ref_p = 5500.0
>>>>gen_vel   = yes
>>>>gen_temp  = 

Re: [gmx-users] rlist

[Faezeh Pousaneh]

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 14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> 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 custom potentials,
> so setting cutoffs is part of the parametrization of that potential itself.
>
> -Justin
>
>
> integrator= md
>>   dt= 0.001
>>   nsteps= 3000
>>   nstxout   = 10   ; save coordinates every 0
>> ps
>>   nstvout   = 10   ; save velocities every 0
>> ps
>>   nstlog= 10   ; update log file every
>>   nstenergy = 10; save energies every
>>   nstxtcout = 10   ; Output frequency for xtc file
>>   xtc-precision = 10   ; precision for xtc file
>>   ns_type   = grid; search neighboring grid cells
>>   nstlist   = 10   ;  fs
>>   pbc   = xyz ; 3-D PBC
>>   rlist  = 0.9 ; short-range neighbor-list
>> cutoff (in nm)
>>   rcoulomb  = 0.9 ; short-range electrostatic
>> cutoff
>> (in nm)
>>   rvdw  = 0.3479  ; short-range van der Waals
>> cutoff
>> (in nm)
>>   coulombtype   = PME-user ; Particle Mesh Ewald for
>> long-range electrostatics
>>   pme_order = 4   ; cubic interpolation
>>   fourierspacing= 0.16; grid spacing for FFT
>>   vdw-type  = user
>>   Tcoupl= berendsen   ; modified Berendsen thermostat
>>   tc-grps   = co2   rest   ; two coupling groups -
>> more accurate
>>   tau_t =  0.1   0.1 ; time constant, in ps
>>   ref_t =  179.8  179.8 ; reference temperature, one
>> for
>> each group, in K
>>   ;tc-grps  = system
>> cutoff-scheme  =group
>>   energygrps= co2 rest
>>   Pcoupl=  berendsen ;Parrinello-Rahman
>>   Pcoupltype= Isotropic
>>   tau_p = 1.0
>>   compressibility   = 6.2e-5
>>   ref_p = 5500.0
>>   gen_vel   = yes
>>   gen_temp  = 179.8
>>   gen_seed  = 712349
>>   DispCorr  =no;  EnerPres; account for cut-off vdW
>> scheme
>>   constraints   = all-bonds   ; all bonds constrained (fixed
>> length)
>>   continuation  = no ; Restarting after NPT
>>   constraint-algorithm  =  lincs   ; holonomic constraints
>>   lincs_iter= 1   ; accuracy of LINCS
>>   lincs_order   = 4   ; also related to accuracy
>> Best regards
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] rlist

[Faezeh Pousaneh]

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= 3000
 nstxout   = 10   ; save coordinates every 0 ps
 nstvout   = 10   ; save velocities every 0 ps
 nstlog= 10   ; update log file every
 nstenergy = 10; save energies every
 nstxtcout = 10   ; Output frequency for xtc file
 xtc-precision = 10   ; precision for xtc file
 ns_type   = grid; search neighboring grid cells
 nstlist   = 10   ;  fs
 pbc   = xyz ; 3-D PBC
 rlist  = 0.9 ; short-range neighbor-list
cutoff (in nm)
 rcoulomb  = 0.9 ; short-range electrostatic cutoff
(in nm)
 rvdw  = 0.3479  ; short-range van der Waals cutoff
(in nm)
 coulombtype   = PME-user ; Particle Mesh Ewald for
long-range electrostatics
 pme_order = 4   ; cubic interpolation
 fourierspacing= 0.16; grid spacing for FFT
 vdw-type  = user
 Tcoupl= berendsen   ; modified Berendsen thermostat
 tc-grps   = co2   rest   ; two coupling groups -
more accurate
 tau_t =  0.1   0.1 ; time constant, in ps
 ref_t =  179.8  179.8 ; reference temperature, one for
each group, in K
 ;tc-grps  = system
cutoff-scheme  =group
 energygrps= co2 rest
 Pcoupl=  berendsen ;Parrinello-Rahman
 Pcoupltype= Isotropic
 tau_p = 1.0
 compressibility   = 6.2e-5
 ref_p = 5500.0
 gen_vel   = yes
 gen_temp  = 179.8
 gen_seed  = 712349
 DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
 constraints   = all-bonds   ; all bonds constrained (fixed
length)
 continuation  = no ; Restarting after NPT
 constraint-algorithm  =  lincs   ; holonomic constraints
 lincs_iter= 1   ; accuracy of LINCS
 lincs_order   = 4   ; also related to accuracy
Best regards
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Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

Thanks Justin.
One component I mean system of only one type atom, each atom has two
charged virtual sites. So I can not see from VMD any breaking.


On Dec 17, 2017 8:10 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:



On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:

> Dear Justin,
>
> How can I check that ''input configuration is "broken" across PBC'' ?
>  From vmd it is hard to say, since I only have one component system.
>

What is that one component? If a group of atoms is supposed to be in a
charge group, and it is split across the box, then you need to correct it
with trjconv or (if you are absolutely sure this isn't a problem) override
with grompp -maxwarn (dangerous and generally not wise).

-Justin



> Best regards
>
>
> On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> The sum of the two largest charge group radii (7.984601) is larger than
>>rlist (0.347900).
>> the configuration looks fine across pbc. Everything looks normal.
>> Following is my md. I have user-specified potential so I need to have
>> cut-off values as given below.
>>
>>
>> integrator= md
>>   dt= 0.001
>>   nsteps= 300
>>   nstxout   = 10   ; save coordinates every 0
>> ps
>>   nstvout   = 10   ; save velocities every 0
>> ps
>>   nstlog= 10   ; update log file every
>>   nstenergy = 10; save energies every
>>   nstxtcout = 10   ; Output frequency for xtc file
>>   xtc-precision = 10   ; precision for xtc file
>>   ns_type   = grid; search neighboring grid cells
>>   nstlist   = 10   ;  fs
>>   pbc   = xyz ; 3-D PBC
>>   rlist = 0.3479  ; short-range neighborlist
>> cutoff
>> (in nm)
>>   rcoulomb  = 0.3479 ; short-range electrostatic
>> cutoff (in nm)
>>   rvdw = 0.3479; short-range van der Waals cutoff (in nm)
>>   coulombtype   = PME-user ; Particle Mesh Ewald for
>> long-range electrostatics
>>   pme_order = 4   ; cubic interpolation
>>   fourierspacing= 0.16; grid spacing for FFT
>>   vdw-type  = user
>>   Tcoupl= berendsen   ; modified Berendsen thermostat
>>   tc-grps   = co2   rest   ; two coupling groups -
>> more accurate
>>   tau_t =  0.1   0.1 ; time constant, in ps
>>   ref_t =  179.8  179.8 ; reference temperature, one
>> for each group, in K
>>   ;tc-grps  = system
>> cutoff-scheme  =group
>>   energygrps= co2 rest
>>   Pcoupl= no;Parrinello-Rahman
>>   Pcoupltype= Isotropic
>>   tau_p = 1.0
>>   compressibility   = 6.2e-5
>>   ref_p = 50.0
>>   gen_vel   = yes
>>   gen_temp  = 179.8
>>   gen_seed  = 712349
>>   DispCorr  =no;  EnerPres; account for cut-off vdW
>> scheme
>>   constraints   = all-bonds   ; all bonds constrained (fixed
>> length)
>>   continuation  = no ; Restarting after NPT
>>   constraint-algorithm  =  lincs   ; holonomic constraints
>>   lincs_iter= 1   ; accuracy of LINCS
>>   lincs_order   = 4   ; also related to accuracy
>>
>>
>>
>> Best regards
>>
>>
>> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>>>
>>> Hi,
>>>>
>>>> I get this error only in NVT equlibration step, not in the NPT and
>>>> production steps. Should I worry about it?
>>>>
>>>> In gromacs page it tell the error can come from 4 reasons, but how I can
>>>> recognize which can be mine?
>>>>
>>>> Check the size of your largest charge group, value of rlist, or whether
>>> or not the input configuration is "broken" across PBC.
>>>
>>> -Justin
>>>
>>> http://www.gromacs.org/Documentation/Errors?highlight=docume
>>>
>>>> ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
>>

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

Dear Justin,

How can I check that ''input configuration is "broken" across PBC'' ?
>From vmd it is hard to say, since I only have one component system.


Best regards


On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:

>
> The sum of the two largest charge group radii (7.984601) is larger than
>   rlist (0.347900).
> the configuration looks fine across pbc. Everything looks normal.
> Following is my md. I have user-specified potential so I need to have
> cut-off values as given below.
>
>
> integrator= md
>  dt= 0.001
>  nsteps= 300
>  nstxout   = 10   ; save coordinates every 0 ps
>  nstvout   = 10   ; save velocities every 0 ps
>  nstlog= 10   ; update log file every
>  nstenergy = 10; save energies every
>  nstxtcout = 10   ; Output frequency for xtc file
>  xtc-precision = 10   ; precision for xtc file
>  ns_type   = grid; search neighboring grid cells
>  nstlist   = 10   ;  fs
>  pbc   = xyz ; 3-D PBC
>  rlist = 0.3479  ; short-range neighborlist cutoff
> (in nm)
>  rcoulomb  = 0.3479 ; short-range electrostatic
> cutoff (in nm)
>  rvdw = 0.3479; short-range van der Waals cutoff (in nm)
>  coulombtype   = PME-user ; Particle Mesh Ewald for
> long-range electrostatics
>  pme_order = 4   ; cubic interpolation
>  fourierspacing= 0.16; grid spacing for FFT
>  vdw-type  = user
>  Tcoupl= berendsen   ; modified Berendsen thermostat
>  tc-grps   = co2   rest   ; two coupling groups -
> more accurate
>  tau_t =  0.1   0.1 ; time constant, in ps
>  ref_t =  179.8  179.8 ; reference temperature, one
> for each group, in K
>  ;tc-grps  = system
> cutoff-scheme  =group
>  energygrps= co2 rest
>  Pcoupl= no;Parrinello-Rahman
>  Pcoupltype= Isotropic
>  tau_p = 1.0
>  compressibility   = 6.2e-5
>  ref_p = 50.0
>  gen_vel   = yes
>  gen_temp  = 179.8
>  gen_seed  = 712349
>  DispCorr  =no;  EnerPres; account for cut-off vdW
> scheme
>  constraints   = all-bonds   ; all bonds constrained (fixed
> length)
>  continuation  = no ; Restarting after NPT
>  constraint-algorithm  =  lincs   ; holonomic constraints
>  lincs_iter= 1   ; accuracy of LINCS
>  lincs_order       = 4   ; also related to accuracy
>
>
>
> Best regards
>
>
> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> I get this error only in NVT equlibration step, not in the NPT and
>>> production steps. Should I worry about it?
>>>
>>> In gromacs page it tell the error can come from 4 reasons, but how I can
>>> recognize which can be mine?
>>>
>>
>> Check the size of your largest charge group, value of rlist, or whether
>> or not the input configuration is "broken" across PBC.
>>
>> -Justin
>>
>> http://www.gromacs.org/Documentation/Errors?highlight=docume
>>> ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
>>> _is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>>
>>> Best regards
>>>
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

The sum of the two largest charge group radii (7.984601) is larger than
  rlist (0.347900).
the configuration looks fine across pbc. Everything looks normal. Following
is my md. I have user-specified potential so I need to have cut-off values
as given below.


integrator= md
 dt= 0.001
 nsteps= 300
 nstxout   = 10   ; save coordinates every 0 ps
 nstvout   = 10   ; save velocities every 0 ps
 nstlog= 10   ; update log file every
 nstenergy = 10; save energies every
 nstxtcout = 10   ; Output frequency for xtc file
 xtc-precision = 10   ; precision for xtc file
 ns_type   = grid; search neighboring grid cells
 nstlist   = 10   ;  fs
 pbc   = xyz ; 3-D PBC
 rlist = 0.3479  ; short-range neighborlist cutoff
(in nm)
 rcoulomb  = 0.3479 ; short-range electrostatic
cutoff (in nm)
 rvdw = 0.3479; short-range van der Waals cutoff (in nm)
 coulombtype   = PME-user ; Particle Mesh Ewald for
long-range electrostatics
 pme_order = 4   ; cubic interpolation
 fourierspacing= 0.16; grid spacing for FFT
 vdw-type  = user
 Tcoupl= berendsen   ; modified Berendsen thermostat
 tc-grps   = co2   rest   ; two coupling groups -
more accurate
 tau_t =  0.1   0.1 ; time constant, in ps
 ref_t =  179.8  179.8 ; reference temperature, one for
each group, in K
 ;tc-grps  = system
cutoff-scheme  =group
 energygrps= co2 rest
 Pcoupl= no;Parrinello-Rahman
 Pcoupltype= Isotropic
 tau_p = 1.0
 compressibility   = 6.2e-5
 ref_p = 50.0
 gen_vel   = yes
 gen_temp  = 179.8
 gen_seed  = 712349
 DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
 constraints   = all-bonds   ; all bonds constrained (fixed
length)
 continuation  = no ; Restarting after NPT
 constraint-algorithm  =  lincs   ; holonomic constraints
 lincs_iter= 1   ; accuracy of LINCS
 lincs_order   = 4   ; also related to accuracy



Best regards


On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I get this error only in NVT equlibration step, not in the NPT and
>> production steps. Should I worry about it?
>>
>> In gromacs page it tell the error can come from 4 reasons, but how I can
>> recognize which can be mine?
>>
>
> Check the size of your largest charge group, value of rlist, or whether or
> not the input configuration is "broken" across PBC.
>
> -Justin
>
> http://www.gromacs.org/Documentation/Errors?highlight=
>> documentation#The_sum_of_the_two_largest_charge_group_
>> radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>
>> Best regards
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

Hi,

I get this error only in NVT equlibration step, not in the NPT and
production steps. Should I worry about it?

In gromacs page it tell the error can come from 4 reasons, but how I can
recognize which can be mine?

http://www.gromacs.org/Documentation/Errors?highlight=documentation#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

Best regards
-- 
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Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Please note that the carbon is a virtual site, so has not mass. So the DOF
does not influence of its configurations on average. Besides the angle   of
M--C--M is always 180.

Mark, I compare the results of average distributions not a snapshot.

Justin, the only LJ are from atom C with next molecules in both systems.
(In fact I got the idea from your carbon dioxide tutorial, in which later I
will add two more virtual sites with charges to create a dipole moment for
my atom (e.g C here), but first I must understand this stage)



Best regards


On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand
> my
> > question, I have no charges in systems on any atoms. So the extra DOF do
> > not effect on potential.
> >
>
> Charge has nothing to do with it. The potential is computed from all the
> interactions in the system, which in your case includes LJ. You aren't
> going to generate the same ensemble of configurations in your two cases, so
> you cannot expect to observe the same distribution of potential energy.
>
> Note that it would have been nice to say whether you were comparing a
> distribution of energies or a snapshot. As it is, we are guessing.
>
> Mark
>
> Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > Potential energy is a function of configuration. You can expect the
> same
> > LJ
> > > energy if you compare the same configuration, ie that the distribution
> of
> > > states is identical. But if you would have the same total energy and a
> > > different distribution between PE and KE (because the DOF change) then
> > you
> > > will not sample the same states.
> > >
> > > Mark
> > >
> > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosa...@gmail.com>
> > > wrote:
> > >
> > > > Dear Mark,
> > > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > > energies
> > > > must be the same, yes?
> > > >
> > > >
> > > > Best regards
> > > >
> > > >
> > > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Your systems have different available degrees of freedom, so they
> > > sample
> > > > > difference spaces. The energies you observe reflect that
> difference.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosa...@gmail.com>
> > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I have a system containing of a virtual site of carbon connected
> > > > > > symmetrically to two dummy massive sites (no charge). like :
> > > M---C---M
> > > > > > My problem is the results I get from simulation of this system is
> > not
> > > > > equal
> > > > > > with results of single Carbon system simulation with mass of 2M
> (at
> > > > > exactly
> > > > > > similar conditions)?
> > > > > > They produce different LJ coul energies, I have even tried for
> > > > > non-charged
> > > > > > systems.
> > > > > >
> > > > > > Thank you in advance for help,
> > > > > > Best regards
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > 

Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Potential energy is a function of configuration. You can expect the same LJ
> energy if you compare the same configuration, ie that the distribution of
> states is identical. But if you would have the same total energy and a
> different distribution between PE and KE (because the DOF change) then you
> will not sample the same states.
>
> Mark
>
> On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Dear Mark,
> > thanks, but degrees of freedom goes to kinetic energies, still LJ
> energies
> > must be the same, yes?
> >
> >
> > Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Your systems have different available degrees of freedom, so they
> sample
> > > difference spaces. The energies you observe reflect that difference.
> > >
> > > Mark
> > >
> > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosa...@gmail.com> wrote:
> > >
> > > > Hi,
> > > >
> > > > I have a system containing of a virtual site of carbon connected
> > > > symmetrically to two dummy massive sites (no charge). like :
> M---C---M
> > > > My problem is the results I get from simulation of this system is not
> > > equal
> > > > with results of single Carbon system simulation with mass of 2M (at
> > > exactly
> > > > similar conditions)?
> > > > They produce different LJ coul energies, I have even tried for
> > > non-charged
> > > > systems.
> > > >
> > > > Thank you in advance for help,
> > > > Best regards
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Dear Mark,
thanks, but degrees of freedom goes to kinetic energies, still LJ energies
must be the same, yes?


Best regards


On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Your systems have different available degrees of freedom, so they sample
> difference spaces. The energies you observe reflect that difference.
>
> Mark
>
> On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosa...@gmail.com> wrote:
>
> > Hi,
> >
> > I have a system containing of a virtual site of carbon connected
> > symmetrically to two dummy massive sites (no charge). like :  M---C---M
> > My problem is the results I get from simulation of this system is not
> equal
> > with results of single Carbon system simulation with mass of 2M (at
> exactly
> > similar conditions)?
> > They produce different LJ coul energies, I have even tried for
> non-charged
> > systems.
> >
> > Thank you in advance for help,
> > Best regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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[gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi,

I have a system containing of a virtual site of carbon connected
symmetrically to two dummy massive sites (no charge). like :  M---C---M
My problem is the results I get from simulation of this system is not equal
with results of single Carbon system simulation with mass of 2M (at exactly
similar conditions)?
They produce different LJ coul energies, I have even tried for non-charged
systems.

Thank you in advance for help,
Best regards
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[gmx-users] c_6 and c_12 to zero

[Faezeh Pousaneh]

Hi,

I have a simple system of non-charged diatomic molecule, (A-B).

I expect total LJ interaction energy in such system when we put LJ
parameters of atom B zero (c6 and c12=0)  should be equal with total LJ
energy of a system containing only atom A.
Am I right?

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[gmx-users] virtual site, dummy massive site LJ interactions

[Faezeh Pousaneh]

Hi,

I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:

1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?

2-  Does adding a dummy massive site (no charge, only mass) to atoms of
mono-atomic system, influences on the LJ energy of whole system?

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[gmx-users] virtual site, dummy massive site

[Faezeh Pousaneh]

I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:

1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?

2-  Does adding a dummy massive site (no charge, only mass) to atoms of
mono-atomic system, influences on the LJ energy of whole system?

Best regards
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[gmx-users] (no subject)

[Faezeh Pousaneh]

Hi,

I have a simple system of non-charged diatomic molecule, (A-B).

I expect total LJ interaction energy in such system when we put LJ
parameters of atom B zero (c6 and c12=0)  should be equal with total LJ
energy of a system containing only atom A.
Am I right?

Best regards
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Re: [gmx-users] force fileds gromos and oplsaa

[Faezeh Pousaneh]

Thanks a lot Justin!


Best regards


On Thu, Nov 16, 2017 at 2:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/16/17 8:28 AM, Faezeh Pousaneh wrote:
>
>> Hi
>>
>> sorry for silly question, but I did not find my answer by searching.
>>
>> In gromos force fields, the file nonbonded.itp includes nonbonded
>> parameters for two different atoms, e.g
>>
>> C O 1 2.300953E-03 2.222000E-06
>>
>> while I do not see oplsaa provides parameters for nonbonded interactions
>> of
>> different atoms, why?
>>
>
> The [nonbond_params] section specifies atom pairs for which normal
> combination rules do not apply, e.g. pair-specific Lennard-Jones parameters
> (CHARMM calls these NBFIX, for instance).
>
> Some force fields use them, others don't (and calculate everything via
> combination rules). In the case of OPLS-AA, there are a huge number of atom
> types, more than any other force field (AFAIK), which is essentially doing
> the same thing - there are highly specific parameter optimizations for
> given interactions.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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[gmx-users] force fileds gromos and oplsaa

[Faezeh Pousaneh]

Hi

sorry for silly question, but I did not find my answer by searching.

In gromos force fields, the file nonbonded.itp includes nonbonded
parameters for two different atoms, e.g

C O 1 2.300953E-03 2.222000E-06

while I do not see oplsaa provides parameters for nonbonded interactions of
different atoms, why?




Best regards
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Re: [gmx-users] GROMOS bond-stretching parameters

[Faezeh Pousaneh]

Thank you!


Best regards


On Tue, Nov 14, 2017 at 3:36 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/13/17 5:24 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>> Unfortunately I do not find in Gromos literature what is the third number
>> in front of
>> bond stretching parameters, e.g 1200 below:
>> :
>>
>> ; ICB(H)[N]CB[N] B0[N]
>> #define gb_50.1230  1.6600e+07
>> ; C  - O1200
>>
>> someone please tell me,
>>
>
> It's an integer code from the original GROMOS parameter files. Note that
> it is on a comment line and thus serves no function in GROMACS.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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[gmx-users] GROMOS bond-stretching parameters

[Faezeh Pousaneh]

Hi,
Unfortunately I do not find in Gromos literature what is the third number
in front of
bond stretching parameters, e.g 1200 below:
:

; ICB(H)[N]CB[N] B0[N]
#define gb_50.1230  1.6600e+07
; C  - O1200

someone please tell me,
Best regards
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Re: [gmx-users] only interaction inside the molecule

[Faezeh Pousaneh]

no that is not my answer Yu.

for example I would like to design a molecule e.g. CO2, I would like
oxygens connected to Carbon in each molecule, but do no interact with rest
of system.
I guess I should change the ffbonded.itp in the following:

keep the length bond but change the interaction strength to zero, and then
restrain the bond length in .mpd file.
but I am not sure ?



Best regards


On Thu, Nov 9, 2017 at 10:15 AM, Du, Yu <d...@sioc.ac.cn> wrote:

> Hi,
>
> From your limited information, I suggest you have a look at the Tabulated
> Potentials, www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>
> Best,
> Yu
>
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
>
> > -Original Messages-
> > From: "Faezeh Pousaneh" <fpoosa...@gmail.com>
> > Sent Time: 2017-11-09 16:58:12 (Thursday)
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Cc:
> > Subject: [gmx-users] only interaction inside the molecule
> >
> > Hi,
> >
> > I would like an atom of my molecule only interact (LJ) with its own
> > molecule, not the rest of system, how can I do that?
> >
> > thanks for reply,
> > Best regards
>
>
>
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[gmx-users] only interaction inside the molecule

[Faezeh Pousaneh]

Hi,

I would like an atom of my molecule only interact (LJ) with its own
molecule, not the rest of system, how can I do that?

thanks for reply,
Best regards
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Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

virtual sites plus shell (drude) particle. which unfortunately there is
little information in the manual.


Best regards


On Mon, Nov 6, 2017 at 5:16 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> I think I have my answer to my initial question; how to give an atom a
> dipole? One can use virtual sites.
>
>
> Best regards
>
>
> On Mon, Nov 6, 2017 at 3:03 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
>> David,
>> do you thin that Stockmayer potential can be implemented by
>> user-specified potential?
>>
>>
>> Best regards
>>
>>
>> On Sun, Nov 5, 2017 at 4:18 PM, David van der Spoel <sp...@xray.bmc.uu.se
>> > wrote:
>>
>>> On 05/11/17 16:07, Faezeh Pousaneh wrote:
>>>
>>>> Yes, exactly. But my atom is uncharged sphere, I'll bring two similar
>>>> size
>>>> and similar mass (+ -) ions inside the sphere. So rotation will not
>>>> happen
>>>> then for atom.
>>>>
>>>
>>> If you simulate multiple such spheres they will behave like a Stockmayer
>>> dipolar fluid.
>>>
>>>
>>>>
>>>> On Nov 5, 2017 16:00, "David van der Spoel" <sp...@xray.bmc.uu.se>
>>>> wrote:
>>>>
>>>> On 05/11/17 15:54, Faezeh Pousaneh wrote:
>>>>
>>>> So I guess the only solution can be:
>>>>>
>>>>> I take two small ions bring them inside original atom, parametrize
>>>>> their
>>>>> interactions with each other and the initial atom such that they stick
>>>>> inside the atom.
>>>>> What do you think?
>>>>>
>>>>> In fact you are then creating a small molecule, like C=O. Nothing wrong
>>>> with that, but you are also creating particles with a mass, which means
>>>> the
>>>> "atom" get rotational properties.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Best regards
>>>>>
>>>>>
>>>>> On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <
>>>>> sp...@xray.bmc.uu.se>
>>>>> wrote:
>>>>>
>>>>> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>>>>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>>
>>>>>>> I have an uncharged atom, and I would like to give it a dipole. Any
>>>>>>> suggestion?
>>>>>>>
>>>>>>> impossible in gromacs.
>>>>>>>
>>>>>>
>>>>>>
>>>>>> Best regards
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>> http://www.icm.uu.se
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>> http://www.icm.uu.se
>>> --
>>> Gromacs Users mailing list
>>>
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>>> /Mailing_Lists/GMX-Users_List before posting!
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>
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Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

I think I have my answer to my initial question; how to give an atom a
dipole? One can use virtual sites.


Best regards


On Mon, Nov 6, 2017 at 3:03 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> David,
> do you thin that Stockmayer potential can be implemented by user-specified
> potential?
>
>
> Best regards
>
>
> On Sun, Nov 5, 2017 at 4:18 PM, David van der Spoel <sp...@xray.bmc.uu.se>
> wrote:
>
>> On 05/11/17 16:07, Faezeh Pousaneh wrote:
>>
>>> Yes, exactly. But my atom is uncharged sphere, I'll bring two similar
>>> size
>>> and similar mass (+ -) ions inside the sphere. So rotation will not
>>> happen
>>> then for atom.
>>>
>>
>> If you simulate multiple such spheres they will behave like a Stockmayer
>> dipolar fluid.
>>
>>
>>>
>>> On Nov 5, 2017 16:00, "David van der Spoel" <sp...@xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 05/11/17 15:54, Faezeh Pousaneh wrote:
>>>
>>> So I guess the only solution can be:
>>>>
>>>> I take two small ions bring them inside original atom, parametrize their
>>>> interactions with each other and the initial atom such that they stick
>>>> inside the atom.
>>>> What do you think?
>>>>
>>>> In fact you are then creating a small molecule, like C=O. Nothing wrong
>>> with that, but you are also creating particles with a mass, which means
>>> the
>>> "atom" get rotational properties.
>>>
>>>
>>>
>>>
>>>
>>>> Best regards
>>>>
>>>>
>>>> On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <
>>>> sp...@xray.bmc.uu.se>
>>>> wrote:
>>>>
>>>> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> I have an uncharged atom, and I would like to give it a dipole. Any
>>>>>> suggestion?
>>>>>>
>>>>>> impossible in gromacs.
>>>>>>
>>>>>
>>>>>
>>>>> Best regards
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>>> http://www.icm.uu.se
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>>>>
>>>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>> send a mail to gmx-users-requ...@gromacs.org.
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>
>
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Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

David,
do you thin that Stockmayer potential can be implemented by user-specified
potential?


Best regards


On Sun, Nov 5, 2017 at 4:18 PM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> On 05/11/17 16:07, Faezeh Pousaneh wrote:
>
>> Yes, exactly. But my atom is uncharged sphere, I'll bring two similar size
>> and similar mass (+ -) ions inside the sphere. So rotation will not
>> happen
>> then for atom.
>>
>
> If you simulate multiple such spheres they will behave like a Stockmayer
> dipolar fluid.
>
>
>>
>> On Nov 5, 2017 16:00, "David van der Spoel" <sp...@xray.bmc.uu.se> wrote:
>>
>> On 05/11/17 15:54, Faezeh Pousaneh wrote:
>>
>> So I guess the only solution can be:
>>>
>>> I take two small ions bring them inside original atom, parametrize their
>>> interactions with each other and the initial atom such that they stick
>>> inside the atom.
>>> What do you think?
>>>
>>> In fact you are then creating a small molecule, like C=O. Nothing wrong
>> with that, but you are also creating particles with a mass, which means
>> the
>> "atom" get rotational properties.
>>
>>
>>
>>
>>
>>> Best regards
>>>
>>>
>>> On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <
>>> sp...@xray.bmc.uu.se>
>>> wrote:
>>>
>>> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>>>
>>>>
>>>> Hi,
>>>>
>>>>>
>>>>> I have an uncharged atom, and I would like to give it a dipole. Any
>>>>> suggestion?
>>>>>
>>>>> impossible in gromacs.
>>>>>
>>>>
>>>>
>>>> Best regards
>>>>>
>>>>>
>>>>>
>>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>
>>>>
>>>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] non-neutral system

[Faezeh Pousaneh]

Hi Justin,

I have a system of 500 Argon fluid each given a charge +0.20 (vdW
cut-off=0.8 nm). So I expect the system to have total positive coulomb
potential (repulsion). Below are simualtion results of PME and cut-off:


PME coulomb results:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2217.86   0.3424.5444  -0.214063
(kJ/mol)
Coulomb (SR)   993.008   0.145.39276  -0.435068  (kJ/mol)
Coul. recip.   -11192.7   0.159.86392  -0.470106
(kJ/mol)
Potential  -12417.50.633.2669   -1.11921
(kJ/mol)
Kinetic En. 1224.39   0.4444.2301   -2.79584
(kJ/mol)
Total Energy  -11193.1   0.9454.8503   -3.91503
(kJ/mol)
Conserved En.  -176697101446.14   -5008.59  (kJ/mol)
Temperature   196.74  0.0717.10709  -0.449246  (K)




Cut-off coulomb results (0.8 nm):

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
LJ (SR)-2231.64   0.5824.27352.05241
(kJ/mol)
Coulomb (SR)  94520.24.7221.879   -9.05937  (kJ/mol)
Potential   92288.54.5217.531   -7.00686
(kJ/mol)
Kinetic En.1257.31   0.4345.3804   0.778738
(kJ/mol)
Total Energy  93545.94.1221.992   -6.22759  (kJ/mol)
Conserved En. 518736  481842.2 283452  (kJ/mol)
Temperature197.031  0.0697.29193   -0.125132  (K)













Best regards


On Mon, Nov 6, 2017 at 1:06 PM, João Henriques <joao.m.a.henriq...@gmail.com
> wrote:

> Hi Johannes,
>
> I just meant that from a purely theoretical point of view, it needs to be
> neutral. This has to do with the convergence of the outer infinite series,
> as the paper Micholas linked clearly states. I sincerely hope I'm not
> botching this up, but this is the conclusion I've withdrawn from reading
> the literature. Now, if the software implementation contains some tricks to
> account for this, that I'm not familiar with and will therefore leave that
> discussion for someone else more acquainted with it.
>
> Cheers,
> J
>
>
>
> On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
> j.herm...@lrz.tu-muenchen.de> wrote:
>
> > Hey Joao,
> >
> > are you sure? I think PME will introduce a neutralizing background
> charge?
> >
> > All the best
> >
> > Johannes
> >
> >
> >
> > On 06.11.2017 11:57, João Henriques wrote:
> >
> >> ​Hi,
> >>
> >> You shouldn't use PME without neutralizing the system's charge. ​It's a
> >> limitation of the Ewald summation. Take a look at the literature for
> >> further details.
> >>
> >> I don't know much about viscosity, so I'll leave that for someone else.
> >>
> >> Cheers,
> >> J
> >>
> >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I  have a system containing similar charged atoms. So the total charge
> is
> >>> not zero.
> >>>
> >>> Simulation results with cut-off coulomb seems reasonable,  but using
> PME
> >>> they are wrong (total columb potential is negative value which must be
> >>> positive). Any idea why?
> >>>
> >>> If I use counter-ions to neutralize the system, I am afraid the
> >>> properties
> >>> I am looking for (viscosity) will be influenced.
> >>>
> >>> Best regards
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at http://www.gromacs.org/
> >>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>> * For (un)subscribe requests visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> > --
> > __
> > *Technische Universität München*
> > *Johannes Hermann, M.Sc.*
> > Lehrstuhl für Bioverfahrenstechnik
> > Boltzmannstr. 15
> > D-85748 Garching
> > Tel: +49 8928915730
> > Fax: +49 8928915714
> >
> > Email: j.herm...@lrz.tum.de
> > http://www.biovt.mw.tum.de/
> >
> >
> >

Re: [gmx-users] non-neutral system

[Faezeh Pousaneh]

Thank you guys.

Johanns, I think one must add counter-ions by himself (which I do not
want), as written here
http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge





Best regards


On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hey Joao,
>
> are you sure? I think PME will introduce a neutralizing background charge?
>
> All the best
>
> Johannes
>
>
>
> On 06.11.2017 11:57, João Henriques wrote:
>
>> ​Hi,
>>
>> You shouldn't use PME without neutralizing the system's charge. ​It's a
>> limitation of the Ewald summation. Take a look at the literature for
>> further details.
>>
>> I don't know much about viscosity, so I'll leave that for someone else.
>>
>> Cheers,
>> J
>>
>> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> I  have a system containing similar charged atoms. So the total charge is
>>> not zero.
>>>
>>> Simulation results with cut-off coulomb seems reasonable,  but using PME
>>> they are wrong (total columb potential is negative value which must be
>>> positive). Any idea why?
>>>
>>> If I use counter-ions to neutralize the system, I am afraid the
>>> properties
>>> I am looking for (viscosity) will be influenced.
>>>
>>> Best regards
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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[gmx-users] non-neutral system

[Faezeh Pousaneh]

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

Best regards
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Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

Yes, exactly. But my atom is uncharged sphere, I'll bring two similar size
and similar mass (+ -) ions inside the sphere. So rotation will not  happen
then for atom.


On Nov 5, 2017 16:00, "David van der Spoel" <sp...@xray.bmc.uu.se> wrote:

On 05/11/17 15:54, Faezeh Pousaneh wrote:

> So I guess the only solution can be:
>
> I take two small ions bring them inside original atom, parametrize their
> interactions with each other and the initial atom such that they stick
> inside the atom.
> What do you think?
>
In fact you are then creating a small molecule, like C=O. Nothing wrong
with that, but you are also creating particles with a mass, which means the
"atom" get rotational properties.




>
> Best regards
>
>
> On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <sp...@xray.bmc.uu.se>
> wrote:
>
> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>>
>> Hi,
>>>
>>> I have an uncharged atom, and I would like to give it a dipole. Any
>>> suggestion?
>>>
>>> impossible in gromacs.
>>
>>
>>> Best regards
>>>
>>>
>>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>

-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] dipole on an atom

[Faezeh Pousaneh]

So I guess the only solution can be:

I take two small ions bring them inside original atom, parametrize their
interactions with each other and the initial atom such that they stick
inside the atom.
What do you think?


Best regards


On Sun, Nov 5, 2017 at 3:42 PM, David van der Spoel <sp...@xray.bmc.uu.se>
wrote:

> On 04/11/17 19:19, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I have an uncharged atom, and I would like to give it a dipole. Any
>> suggestion?
>>
> impossible in gromacs.
>
>>
>> Best regards
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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[gmx-users] dipole on an atom

[Faezeh Pousaneh]

Hi,

I have an uncharged atom, and I would like to give it a dipole. Any
suggestion?

Best regards
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[gmx-users] viscosity from periodic perturbation method

[Faezeh Pousaneh]

Hi,

My simulation results for viscosity calculation strongly depends on the
chosen amplitudes of the acceleration profiles in the .mdp file (!?). How
to estimate acceleration amplitude values?

appreciate if someone can answer,
Best regards
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Re: [gmx-users] User-specified potential functions

[Faezeh Pousaneh]

Solved!!

the constant can be added to the table, to g(r) or h(r).


Best regards


On Tue, Oct 24, 2017 at 7:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:

> Hi,
>
> I created a table for my own potential which has a 'constant' value. I
> added it to the g(r) or h(r) functions in the table, but it gives incorrect
> results.
> I also can not shift the potential after simulation, since the x>cut-off
> will be also shifted.
>
> Any suggestion?
>
> Best regards
>
>
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[gmx-users] User-specified potential functions

[Faezeh Pousaneh]

Hi,

I created a table for my own potential which has a 'constant' value. I
added it to the g(r) or h(r) functions in the table, but it gives incorrect
results.
I also can not shift the potential after simulation, since the x>cut-off
will be also shifted.

Any suggestion?

Best regards
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[gmx-users] non-zero total charge

[Faezeh Pousaneh]

Hi,

I am simulating one component system (tabulated potential), and they have
similar charge. So the total charge of the system is non-zero. The program
properly works. Should I still worry?

Thanks for answer
Best regards
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Re: [gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

I see, thanks Mark,


Best regards


On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> To reproduce the training data for each forcefield, e.g. some experimental
> or other computational result, e.g. the density of argon gas under various
> conditions. Details of what and how do vary with the force field, are are
> documented in its literature, of course.
>
> Mark
>
> On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
>> Apart from my own simulation, I do no understand how the values of C6 and
>> C12 are obtained for each atoms in ''atometypes'' in force fields, could
>> you tell me?
>>
>>
>> Best regards
>>
>>
>> On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett <w.barn...@columbia.edu>
>> wrote:
>>
>>>
>>>
>>> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
>>> wrote:
>>>
>>>> Thank you Wes and Mark,
>>>>
>>>> Wes, that is what I am trying to do. However, still have problem.
>>>> I do not know how to derive sigma, epsilon (or C6 and C12) for my
>>>> particle?
>>>> How the force fields have obtained C6 and C12 values in their .itp
>>>> files for each atom?
>>>>
>>>
>>> That depends on what the purpose of your simulation is. If you're just
>>> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
>>> could be reasonable.
>>>
>>>
>>>>
>>>>
>>>> Best regards
>>>>
>>>>
>>>> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barn...@columbia.edu>
>>>> wrote:
>>>>
>>>>> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
>>>>> wrote:
>>>>>
>>>>> > Hi Mark
>>>>> >
>>>>> > I have a given function for pseudo hard-sphere potential, which has
>>>>> > different powers than LJ and a constant. I have to insert the
>>>>> constant in
>>>>> > order to properly define the cut-off for my hard spheres.
>>>>> > I just realized that I can use "user-specified potential". I guess I
>>>>> can
>>>>> > include the constant there, yes?
>>>>> >
>>>>> > One more thing, I need to have my own particles, spheres with a
>>>>> diameter
>>>>> > "a". How can I have them in gromacs?
>>>>> > .
>>>>> >
>>>>>
>>>>> This should get you started in generating your own tables:
>>>>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>>>>>
>>>>> If all you're looking to do is create repulsive spheres (again, not
>>>>> true
>>>>> hard spheres as Mark said; just removing attractions from the
>>>>> interactions), then cut off your interactions at 2^(1/6)*sigma and
>>>>> shift
>>>>> the potential at the cutoff to zero in your table. If you want
>>>>> different
>>>>> size spheres you need to subtract an additional term from r in the
>>>>> denominators of the c6 and c12 terms.
>>>>>
>>>>> --
>>>>> James "Wes" Barnett
>>>>> Postdoctoral Research Scientist
>>>>> Department of Chemical Engineering
>>>>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
>>>>> Columbia University
>>>>> w.barn...@columbia.edu
>>>>> http://wbarnett.us
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> James "Wes" Barnett
>>> Postdoctoral Research Scientist
>>> Department of Chemical Engineering
>>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
>>> Columbia University
>>> w.barn...@columbia.edu
>>> http://wbarnett.us
>>>
>>
>>
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Re: [gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

Apart from my own simulation, I do no understand how the values of C6 and
C12 are obtained for each atoms in ''atometypes'' in force fields, could
you tell me?


Best regards


On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett <w.barn...@columbia.edu> wrote:

>
>
> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
>> Thank you Wes and Mark,
>>
>> Wes, that is what I am trying to do. However, still have problem.
>> I do not know how to derive sigma, epsilon (or C6 and C12) for my
>> particle?
>> How the force fields have obtained C6 and C12 values in their .itp files
>> for each atom?
>>
>
> That depends on what the purpose of your simulation is. If you're just
> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
> could be reasonable.
>
>
>>
>>
>> Best regards
>>
>>
>> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barn...@columbia.edu>
>> wrote:
>>
>>> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
>>> wrote:
>>>
>>> > Hi Mark
>>> >
>>> > I have a given function for pseudo hard-sphere potential, which has
>>> > different powers than LJ and a constant. I have to insert the constant
>>> in
>>> > order to properly define the cut-off for my hard spheres.
>>> > I just realized that I can use "user-specified potential". I guess I
>>> can
>>> > include the constant there, yes?
>>> >
>>> > One more thing, I need to have my own particles, spheres with a
>>> diameter
>>> > "a". How can I have them in gromacs?
>>> > .
>>> >
>>>
>>> This should get you started in generating your own tables:
>>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>>>
>>> If all you're looking to do is create repulsive spheres (again, not true
>>> hard spheres as Mark said; just removing attractions from the
>>> interactions), then cut off your interactions at 2^(1/6)*sigma and shift
>>> the potential at the cutoff to zero in your table. If you want different
>>> size spheres you need to subtract an additional term from r in the
>>> denominators of the c6 and c12 terms.
>>>
>>> --
>>> James "Wes" Barnett
>>> Postdoctoral Research Scientist
>>> Department of Chemical Engineering
>>> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
>>> Columbia University
>>> w.barn...@columbia.edu
>>> http://wbarnett.us
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
>
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Re: [gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

Thank you Wes and Mark,

Wes, that is what I am trying to do. However, still have problem.
I do not know how to derive sigma, epsilon (or C6 and C12) for my particle?
How the force fields have obtained C6 and C12 values in their .itp files
for each atom?


Best regards


On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barn...@columbia.edu> wrote:

> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi Mark
> >
> > I have a given function for pseudo hard-sphere potential, which has
> > different powers than LJ and a constant. I have to insert the constant in
> > order to properly define the cut-off for my hard spheres.
> > I just realized that I can use "user-specified potential". I guess I can
> > include the constant there, yes?
> >
> > One more thing, I need to have my own particles, spheres with a diameter
> > "a". How can I have them in gromacs?
> > .
> >
>
> This should get you started in generating your own tables:
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>
> If all you're looking to do is create repulsive spheres (again, not true
> hard spheres as Mark said; just removing attractions from the
> interactions), then cut off your interactions at 2^(1/6)*sigma and shift
> the potential at the cutoff to zero in your table. If you want different
> size spheres you need to subtract an additional term from r in the
> denominators of the c6 and c12 terms.
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

Hi Mark

I have a given function for pseudo hard-sphere potential, which has
different powers than LJ and a constant. I have to insert the constant in
order to properly define the cut-off for my hard spheres.
I just realized that I can use "user-specified potential". I guess I can
include the constant there, yes?

One more thing, I need to have my own particles, spheres with a diameter
"a". How can I have them in gromacs?
.

On Oct 9, 2017 3:44 PM, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a
constant,
> (to remove attraction), how can I change the function?
>
>
> Best regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi Mark,

I have a given function for pseudo hard-sphere potential, which has
different powers than LJ and a constant. I have to insert the constant in
order to properly define the cut-off for my hard spheres.
I just realized that I can use "user-specified potential". I guess I can
include the constant there, yes?

One more thing, I need to have my own particles, spheres with a diameter
"a". How can I have them in gromacs?

On Oct 9, 2017 3:44 PM, "Mark Abraham" <mark.j.abra...@gmail.com> wrote:

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a
constant,
> (to remove attraction), how can I change the function?
>
>
> Best regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi,

I would like to shift the LJ interaction between my particle by a constant,
(to remove attraction), how can I change the function?


Best regards
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[gmx-users] not specific molecule or atom

[Faezeh Pousaneh]

Hi

I am trying to simulate 'sphere particles' with a diameters with specific
interactions among them. How can I have my own particles not a defined
molecules or atoms in the force fields.

thanks for answer,
Best regards
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Re: [gmx-users] Cutting simulatio box

[Faezeh Pousaneh]

You are absolutely right.

So, my objective:
I have a phase separation of a two-component system, and my aim is to
obtain the 'chemical potential' at each phase (which I know they must be
equal, since there is equilibrium). The method I've chosen is summation of
'ideal' and 'excess' chemical potentials, which the latter is obtained
through interaction of single molecule with the rest of molecules at that
phase.





Best regards


On Mon, Jul 18, 2016 at 1:25 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi Faezeh,
>
> It helps if you begin with stating your objective and context, rather than
> asking for the solution to what you think is the critical issue in what you
> think is the solution of what you think your problem is. If you ask for
> water in a slab, you get an answer for water in a slab. Apparently you want
> a specific water molecule. Then you ask for a 'phase', which usually
> involves many particles, but it appears that it's that same single
> molecule? That changes matters quite a bit, as whatever you're going to
> look at is going to be pretty noise.
>
> What is your objective?
>
> Cheers,
>
> Tsjerk
>
> On Mon, Jul 18, 2016 at 1:10 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi Tsjerk,
> >
> > That option seemed complicated in my case, as my previous discussion with
> > Mark (titled: g_select, only 'one' water within z>=10 and z<=10.1).
> Since I
> > need the energy between 'single' molecule at specific 'z' of the box
> > indicating the phases .
> >
> > So I think my given way is easier, but not sure if the reruns goes like
> the
> > original simulations?
> >
> >
> > Best regards
> >
> >
> > On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> > wrote:
> >
> > > Hi Faezeh,
> > >
> > > You could use gmx select to make groups for the two phases and then
> > perform
> > > a rerun with these new groups as energy_grps. That would give you the
> > > within and between group energies.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" <fpoosa...@gmail.com>
> wrote:
> > >
> > > Hi,
> > >
> > > I have a Phase-separation in my simulation result. I need to find
> energy
> > > between molecules at each phase. Can I cut the box into small boxes,
> each
> > > having one phase, and then by extension the run (with similar setting
> as
> > > original) obtain the energies at each phase?
> > >
> > > Thank you!
> > > Best regards
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
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> > send
> > > a mail to gmx-users-requ...@gromacs.org.
> > > --
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> > >
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> > > posting!
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> > >
> > --
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> >
>
>
>
> --
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Re: [gmx-users] Cutting simulatio box

[Faezeh Pousaneh]

Hi Tsjerk,

That option seemed complicated in my case, as my previous discussion with
Mark (titled: g_select, only 'one' water within z>=10 and z<=10.1). Since I
need the energy between 'single' molecule at specific 'z' of the box
indicating the phases .

So I think my given way is easier, but not sure if the reruns goes like the
original simulations?


Best regards


On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:

> Hi Faezeh,
>
> You could use gmx select to make groups for the two phases and then perform
> a rerun with these new groups as energy_grps. That would give you the
> within and between group energies.
>
> Hope it helps,
>
> Tsjerk
>
> On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:
>
> Hi,
>
> I have a Phase-separation in my simulation result. I need to find energy
> between molecules at each phase. Can I cut the box into small boxes, each
> having one phase, and then by extension the run (with similar setting as
> original) obtain the energies at each phase?
>
> Thank you!
> Best regards
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] Cutting simulatio box

[Faezeh Pousaneh]

Hi,

I have a Phase-separation in my simulation result. I need to find energy
between molecules at each phase. Can I cut the box into small boxes, each
having one phase, and then by extension the run (with similar setting as
original) obtain the energies at each phase?

Thank you!
Best regards
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Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Faezeh Pousaneh]

Thanks Mark, but I hardly believe that helps. What you suggest can work for
only one frame. But I need a selection which works at the same time for all
frames (in my loop over trajectory), where there are no molecules at some
frames or two or more at others (in z >= 10 and z <= 10.1).


Best regards


On Fri, Jul 15, 2016 at 6:48 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> If your criterion could satisfy more than one molecule but you for example
> only want the first one, then you can likely create a second selection
> where you filter out from the first selection the molecule or atom indices
> that suit you. I assume that can be done in one call to gmx select, but the
> details are an exercise for the reader :-P
>
> Mark
>
> On Fri, 15 Jul 2016 15:52 Faezeh Pousaneh <fpoosa...@gmail.com> wrote:
>
> > I undrestand my command is not correct for having one water. So it is my
> > question how to change the command to have a single molecule?
> >
> >
> >
> > Best regards
> >
> >
> > On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:
> > >
> > >> Hi,
> > >>
> > >> I want to select only a 'single' water molecule at specific part of my
> > >> simulation box.
> > >> So I try:
> > >>
> > >> g_select-selrpos whole_mol_com
> > >>
> > >> and select
> > >>
> > >> resname SOL and z >= 10 and z <= 10.1
> > >>
> > >> But depending on time frame I get more than one molecules or sometimes
> > no
> > >> molecules. How can I fix it?
> > >>
> > >>
> > > Why do you think that the selection criteria should always return
> exactly
> > > one water?  I see no reason to think that based on what your syntax
> > > specifies.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Faezeh Pousaneh]

I undrestand my command is not correct for having one water. So it is my
question how to change the command to have a single molecule?



Best regards


On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I want to select only a 'single' water molecule at specific part of my
>> simulation box.
>> So I try:
>>
>> g_select-selrpos whole_mol_com
>>
>> and select
>>
>> resname SOL and z >= 10 and z <= 10.1
>>
>> But depending on time frame I get more than one molecules or sometimes no
>> molecules. How can I fix it?
>>
>>
> Why do you think that the selection criteria should always return exactly
> one water?  I see no reason to think that based on what your syntax
> specifies.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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[gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Faezeh Pousaneh]

Hi,

I want to select only a 'single' water molecule at specific part of my
simulation box.
So I try:

g_select-selrpos whole_mol_com

and select

resname SOL and z >= 10 and z <= 10.1

But depending on time frame I get more than one molecules or sometimes no
molecules. How can I fix it?

Thank you!
Best regards
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Dear Justin,

I have a question regarding my last question (below which was 'obtaining
energy for different selections').

My selection is a molecule within specific z of the box. I want the
selected z remains fix for whole energy calculation. I realized that mdrun
-rerun does not update the position of the selection for all frames.
Therefore, I guess one needs first to make a 'dynamic' selection from
g_select. The resulted index file then contains  selections for all frames
written frame by frame. Now, I suppose one can go for mdrun -rerun with the
given index file. However, my question now is how properly re-name the
energy groups in .mdp file according to the index file which has so many
frames?

Thank you for help.

Best regards


On Fri, Jul 1, 2016 at 4:20 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Thank you again :)
>
>
> Best regards
>
>
> On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 7/1/16 10:05 AM, Faezeh Pousaneh wrote:
>>
>>> Thank you Justin and Mark for the help. I could obtain.
>>>
>>> More details for someone with similar question:
>>>
>>> 1- First I defined the molecules (resnr 1 to 4) I wanted to look at
>>> (from
>>> existing simulation: production.tpr  6000wat.gro) :
>>>
>>> g_select -f 6000wat.gro -s production.tpr -on index.ndx
>>>
>>> resnr 1 to 4
>>>
>>> resnr 5 to 6000
>>>
>>> (all other renaming molecules also must be defined as next group,
>>> resnr 5 to 6000)
>>>
>>> 2- Then I looked at the name of groups created in the index file and
>>> changed the current .mdp file to include those groups:
>>>
>>>
>> For the sake of correctness in the archive, don't do this:
>>
>> tc-grps   =  resnr_5_to_6000 resnr_1_to_4
>>>
>>
>> For the purpose of a re-run, tc-grps being split this way has no effect.
>> But one should absolutely not divide thermostatting groups in this way.
>>
>> I feel it is important to point out so that (1) people don't make this a
>> common practice and (2) you don't start re-using .mdp files with these
>> settings.
>>
>> This is all you need to accomplish what you want in terms of the energy:
>>
>> energygrps=  resnr_5_to_6000resnr_1_to_4
>>>
>>>
>> The rest of the .mdp file should be the same as your original run.
>>
>> -Justin
>>
>>
>> 3- Finally rerun
>>>
>>> grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
>>> mdrun -rerun traj.xtc -s new.tpr -mn index.ndx
>>>
>>> 4- So, if you now run g_energy you'll find those specified groups
>>> energies.
>>>
>>>
>>>
>>> Best regards
>>>
>>>
>>> On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>>>>
>>>> Thank you both, I am close to solve it. The remaining problem is when I
>>>>> mdrun -rerun, it tells the number of atoms in old trajectory is not the
>>>>> same as chosen index file.
>>>>>
>>>>> Number of atoms in trajectory (24000) does not match the run input file
>>>>>
>>>>>>
>>>>>> (16)
>>>>>
>>>>>
>>>>> Your .tpr file needs to contain the same system that you ran before.
>>>> The
>>>> only thing that changes is the energygrps setting in the .mdp file.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> can you help me?
>>>>
>>>>> Best regards
>>>>>
>>>>>
>>>>> On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com
>>>>> >
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> Yes as Justin says, a group is a few molecules that you selected :-)
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
>>>>>>>
>>>>>>> Thank you Mark, I see. But what is the solution then? The way you
>>>>>>>>
>>>>>>>> propos

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you again :)


Best regards


On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/1/16 10:05 AM, Faezeh Pousaneh wrote:
>
>> Thank you Justin and Mark for the help. I could obtain.
>>
>> More details for someone with similar question:
>>
>> 1- First I defined the molecules (resnr 1 to 4) I wanted to look at  (from
>> existing simulation: production.tpr  6000wat.gro) :
>>
>> g_select -f 6000wat.gro -s production.tpr -on index.ndx
>>
>> resnr 1 to 4
>>
>> resnr 5 to 6000
>>
>> (all other renaming molecules also must be defined as next group,
>> resnr 5 to 6000)
>>
>> 2- Then I looked at the name of groups created in the index file and
>> changed the current .mdp file to include those groups:
>>
>>
> For the sake of correctness in the archive, don't do this:
>
> tc-grps   =  resnr_5_to_6000 resnr_1_to_4
>>
>
> For the purpose of a re-run, tc-grps being split this way has no effect.
> But one should absolutely not divide thermostatting groups in this way.
>
> I feel it is important to point out so that (1) people don't make this a
> common practice and (2) you don't start re-using .mdp files with these
> settings.
>
> This is all you need to accomplish what you want in terms of the energy:
>
> energygrps=  resnr_5_to_6000resnr_1_to_4
>>
>>
> The rest of the .mdp file should be the same as your original run.
>
> -Justin
>
>
> 3- Finally rerun
>>
>> grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
>> mdrun -rerun traj.xtc -s new.tpr -mn index.ndx
>>
>> 4- So, if you now run g_energy you'll find those specified groups
>> energies.
>>
>>
>>
>> Best regards
>>
>>
>> On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>>>
>>> Thank you both, I am close to solve it. The remaining problem is when I
>>>> mdrun -rerun, it tells the number of atoms in old trajectory is not the
>>>> same as chosen index file.
>>>>
>>>> Number of atoms in trajectory (24000) does not match the run input file
>>>>
>>>>>
>>>>> (16)
>>>>
>>>>
>>>> Your .tpr file needs to contain the same system that you ran before.
>>> The
>>> only thing that changes is the energygrps setting in the .mdp file.
>>>
>>> -Justin
>>>
>>>
>>> can you help me?
>>>
>>>> Best regards
>>>>
>>>>
>>>> On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>>>
>>>>> Yes as Justin says, a group is a few molecules that you selected :-)
>>>>>
>>>>> Mark
>>>>>
>>>>> On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>>> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
>>>>>>
>>>>>> Thank you Mark, I see. But what is the solution then? The way you
>>>>>>>
>>>>>>> proposed
>>>>>>
>>>>>>
>>>>>>> ''You can make a new .tpr file with those
>>>>>>> energy groups and use mdrun -rerun on the old trajectory, however.''
>>>>>>>
>>>>>>>  is not my answer, since I do not want the energy for a ''group'' of
>>>>>>> molecules, rather for specified combination of few molecules I define
>>>>>>>
>>>>>>> from
>>>>>>
>>>>>> g_select.
>>>>>>>
>>>>>>>
>>>>>>> The only function available is to define energygrps in the .mdp file,
>>>>>> supply an
>>>>>> index file with those groups (e.g. from g_select) and do as Mark says
>>>>>> and
>>>>>> re-calculate those interaction energies with mdrun -rerun on the
>>>>>> existing
>>>>>> trajectory.  The short-range nonbonded interaction energies between
>>>>>> those
>>>>>> groups
>>>>>> will be written to their own terms in a new .edr file.
>>>>>>
>>>>>> -Justin
>>>

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you Justin and Mark for the help. I could obtain.

More details for someone with similar question:

1- First I defined the molecules (resnr 1 to 4) I wanted to look at  (from
existing simulation: production.tpr  6000wat.gro) :

g_select -f 6000wat.gro -s production.tpr -on index.ndx

resnr 1 to 4

resnr 5 to 6000

(all other renaming molecules also must be defined as next group,
resnr 5 to 6000)

2- Then I looked at the name of groups created in the index file and
changed the current .mdp file to include those groups:

tc-grps   =  resnr_5_to_6000 resnr_1_to_4
energygrps=  resnr_5_to_6000resnr_1_to_4

3- Finally rerun

grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx
mdrun -rerun traj.xtc -s new.tpr -mn index.ndx

4- So, if you now run g_energy you'll find those specified groups energies.



Best regards


On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
>
>> Thank you both, I am close to solve it. The remaining problem is when I
>> mdrun -rerun, it tells the number of atoms in old trajectory is not the
>> same as chosen index file.
>>
>> Number of atoms in trajectory (24000) does not match the run input file
>>>
>> (16)
>>
>>
> Your .tpr file needs to contain the same system that you ran before.  The
> only thing that changes is the energygrps setting in the .mdp file.
>
> -Justin
>
>
> can you help me?
>> Best regards
>>
>>
>> On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> Yes as Justin says, a group is a few molecules that you selected :-)
>>>
>>> Mark
>>>
>>> On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
>>>>
>>>>> Thank you Mark, I see. But what is the solution then? The way you
>>>>>
>>>> proposed
>>>>
>>>>>
>>>>> ''You can make a new .tpr file with those
>>>>> energy groups and use mdrun -rerun on the old trajectory, however.''
>>>>>
>>>>>  is not my answer, since I do not want the energy for a ''group'' of
>>>>> molecules, rather for specified combination of few molecules I define
>>>>>
>>>> from
>>>>
>>>>> g_select.
>>>>>
>>>>>
>>>> The only function available is to define energygrps in the .mdp file,
>>>> supply an
>>>> index file with those groups (e.g. from g_select) and do as Mark says
>>>> and
>>>> re-calculate those interaction energies with mdrun -rerun on the
>>>> existing
>>>> trajectory.  The short-range nonbonded interaction energies between
>>>> those
>>>> groups
>>>> will be written to their own terms in a new .edr file.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>> Best regards
>>>>>
>>>>>
>>>>> On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
>>>>>
>>>> mark.j.abra...@gmail.com>
>>>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>>
>>>>>> The .edr file contains only what was written during the simulation,
>>>>>>
>>>>> and
>>>
>>>> that was for any energy groups defined before that run. You're trying
>>>>>>
>>>>> to
>>>
>>>> ask it to make an arbitrary repartition, which it can't do unless it
>>>>>> recorded every component of the energy for every frame (which would
>>>>>>
>>>>> take
>>>
>>>> forever and use lots of disk). You can make a new .tpr file with those
>>>>>> energy groups and use mdrun -rerun on the old trajectory, however.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Hi
>>>>>>>
>>>>>>> Does someone know how to obtain energy between specific molecules in
>>>>>>>
>>>>>> the
>>>>
>>>>> system?
>>>>>>>
>>>>>>> What I did and seems not be correct is:
>>>>>

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you both, I am close to solve it. The remaining problem is when I
mdrun -rerun, it tells the number of atoms in old trajectory is not the
same as chosen index file.

>Number of atoms in trajectory (24000) does not match the run input file
(16)

can you help me?
Best regards


On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Yes as Justin says, a group is a few molecules that you selected :-)
>
> Mark
>
> On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote:
>
> >
> >
> > On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
> > > Thank you Mark, I see. But what is the solution then? The way you
> > proposed
> > >
> > > ''You can make a new .tpr file with those
> > > energy groups and use mdrun -rerun on the old trajectory, however.''
> > >
> > >  is not my answer, since I do not want the energy for a ''group'' of
> > > molecules, rather for specified combination of few molecules I define
> > from
> > > g_select.
> > >
> >
> > The only function available is to define energygrps in the .mdp file,
> > supply an
> > index file with those groups (e.g. from g_select) and do as Mark says and
> > re-calculate those interaction energies with mdrun -rerun on the existing
> > trajectory.  The short-range nonbonded interaction energies between those
> > groups
> > will be written to their own terms in a new .edr file.
> >
> > -Justin
> >
> > >
> > > Best regards
> > >
> > >
> > > On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > >> Hi,
> > >>
> > >> The .edr file contains only what was written during the simulation,
> and
> > >> that was for any energy groups defined before that run. You're trying
> to
> > >> ask it to make an arbitrary repartition, which it can't do unless it
> > >> recorded every component of the energy for every frame (which would
> take
> > >> forever and use lots of disk). You can make a new .tpr file with those
> > >> energy groups and use mdrun -rerun on the old trajectory, however.
> > >>
> > >> Mark
> > >>
> > >> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com>
> > >> wrote:
> > >>
> > >>> Hi
> > >>>
> > >>> Does someone know how to obtain energy between specific molecules in
> > the
> > >>> system?
> > >>>
> > >>> What I did and seems not be correct is:
> > >>> 1- I obtained the molecules I wanted to look at:
> > >>> g_select_mpi -f 600gro.gro -s production.tpr -on
> > >>>
> > >>> 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> > >>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
> > >>>
> > >>> 3- Finally put the created .tpr file as an input for g_energy
> > >>> g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
> > >>>
> > >>> But that is not the solution, since it gives energy for whole system.
> > >>> Best regards
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at
> > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>> posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
> > >>> * For (un)subscribe requests visit
> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-requ...@gromacs.org.
> > >>>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Po

Re: [gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Thank you Mark, I see. But what is the solution then? The way you proposed

''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''

 is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define from
g_select.


Best regards


On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> The .edr file contains only what was written during the simulation, and
> that was for any energy groups defined before that run. You're trying to
> ask it to make an arbitrary repartition, which it can't do unless it
> recorded every component of the energy for every frame (which would take
> forever and use lots of disk). You can make a new .tpr file with those
> energy groups and use mdrun -rerun on the old trajectory, however.
>
> Mark
>
> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi
> >
> > Does someone know how to obtain energy between specific molecules in the
> > system?
> >
> > What I did and seems not be correct is:
> > 1- I obtained the molecules I wanted to look at:
> > g_select_mpi -f 600gro.gro -s production.tpr -on
> >
> > 2- Then I produced a .tpr file for the chosen selection,index.ndx,
> > tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
> >
> > 3- Finally put the created .tpr file as an input for g_energy
> > g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)
> >
> > But that is not the solution, since it gives energy for whole system.
> > Best regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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[gmx-users] Energy between desired selected molecules

[Faezeh Pousaneh]

Hi

Does someone know how to obtain energy between specific molecules in the
system?

What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on

2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr

3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr  (either, g_energy -s tpxout.tpr)

But that is not the solution, since it gives energy for whole system.
Best regards
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Hi Tsjerk

Your approach shows of course the appearance of the phase separation, but I
necessarily need the time evolution of density of one component to see
'how' it reaches the equilibrium obtaining two difference mass fractions.


Best regards.


Best regards


On Fri, Apr 8, 2016 at 12:34 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:

> Hi Tsjerk
>
> I attach a picture what I explicitly want. Your approach shows of course
> the appearance of the phase separation, but I necessarily need the time
> evolution of density of one component to see 'how' it reaches the
> equilibrium by obtaining two difference mass fractions.  .
>
>
> Best regards.
>
>
>
> Best regards
>
>
> On Fri, Apr 8, 2016 at 11:28 AM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
>>
>> Hi Tsjerk,
>>
>> I attach a picture what I explicitly want. Your approach shows of course
>> the appearance of the phase separation, but I necessarily need the time
>> evolution of density of one component to see 'how' it reaches the
>> equilibrium by obtaining two difference mass fractions.
>>
>>
>> Best regards
>>
>>
>> On Thu, Apr 7, 2016 at 10:32 PM, Tsjerk Wassenaar <tsje...@gmail.com>
>> wrote:
>>
>>> Hi Faezeh,
>>>
>>> According to your previous mail, what you want is...
>>>
>>> > I am dealing with phase separation of a two-component system. At the
>>> end
>>> of
>>> > simulation the mixed system phase separate to two phases, one is rich
>>> in
>>> > one component and the other phase is rich with the other component. So
>>> I
>>> > want to see how each component  reachs those fractions by time?
>>>
>>> ... to see how the components phase separate.
>>>
>>> In a maximally mixed state, the number of contacts between species A and
>>> B
>>> in the mixture is maximal, while the number of contacts within the
>>> groups A
>>> and B, respectively, are minimal. Vice-versa, in a completely phase
>>> separated system, the number of contacts between groups is minimal (only
>>> the interface), while the contacts within groups are maximized. So these
>>> numbers should show you the time course and degree of phase separation,
>>> which seems to be what you stated to want. Apparently, you do not want
>>> what
>>> you said you wanted, but maybe we can give it another shot with a
>>> description of what you really want then.
>>>
>>> Best,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> On Thu, Apr 7, 2016 at 6:42 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
>>> wrote:
>>>
>>> > Dear Tsjerk, no that does not give what I want.
>>> >
>>> >
>>> >
>>> > Best regards
>>> >
>>> >
>>> > On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
>>> > wrote:
>>> >
>>> > > Hi Negar,
>>> > >
>>> > > I tried your solution, but still it does not give the density (of
>>> each
>>> > > component) versus time. It gives density versus distance for
>>> different
>>> > > frames. This could be easily done by g_density with an .ndx file. I
>>> need
>>> > to
>>> > > have a plot of density-time for each of the components of the system.
>>> > >
>>> > > Please help...
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > Best regards
>>> > >
>>> > >
>>> > > On Wed, Apr 6, 2016 at 7:13 PM, Tsjerk Wassenaar <tsje...@gmail.com>
>>> > > wrote:
>>> > >
>>> > >> Hi Faezeh,
>>> > >>
>>> > >> You can count the number of contacts within and between groups to
>>> follow
>>> > >> the process over time using gmx mindist.
>>> > >>
>>> > >> Hope it helps,
>>> > >>
>>> > >> Tsjerk
>>> > >> On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com>
>>> wrote:
>>> > >>
>>> > >> > Hi Tsjerk,
>>> > >> >
>>> > >> > Thanks, but my question it is not that simple.
>>> > >> > I am dealing with phase separation of a two-component system. At
>>> the
>>> > >> end of

Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Dear Tsjerk, no that does not give what I want.



Best regards


On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Hi Negar,
>
> I tried your solution, but still it does not give the density (of each
> component) versus time. It gives density versus distance for different
> frames. This could be easily done by g_density with an .ndx file. I need to
> have a plot of density-time for each of the components of the system.
>
> Please help...
>
>
>
>
> Best regards
>
>
> On Wed, Apr 6, 2016 at 7:13 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
>> Hi Faezeh,
>>
>> You can count the number of contacts within and between groups to follow
>> the process over time using gmx mindist.
>>
>> Hope it helps,
>>
>> Tsjerk
>> On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:
>>
>> > Hi Tsjerk,
>> >
>> > Thanks, but my question it is not that simple.
>> > I am dealing with phase separation of a two-component system. At the
>> end of
>> > simulation the mixed system phase separate to two phases, one is rich in
>> > one component and the other phase is rich with the other component. So I
>> > want to see how each component  reachs those fractions by time?
>> >
>> >
>> >
>> > Best regards
>> >
>> >
>> > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com>
>> > wrote:
>> >
>> > > Hi Faezeh,
>> > >
>> > > Using -b/-e flags you can get the density profile over a window of
>> time
>> > (or
>> > > a single frame). Afterwards you can combine the results to have a
>> density
>> > > profile over time.
>> > >
>> > > Hope it helps,
>> > >
>> > > Tsjerk
>> > >
>> > > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
>> > > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > Is it possible to obtain partial density versus time in Gromacs?
>> > > Precisely,
>> > > > I have a system of two components which separate by time. I need the
>> > > > evolution of density of each phase by time?
>> > > >
>> > > > thanks.
>> > > > Best regards
>> > > > --
>> > > > Gromacs Users mailing list
>> > > >
>> > > > * Please search the archive at
>> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > > posting!
>> > > >
>> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > >
>> > > > * For (un)subscribe requests visit
>> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> > > > send a mail to gmx-users-requ...@gromacs.org.
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Tsjerk A. Wassenaar, Ph.D.
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
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>> > >
>> > --
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Hi Negar,

I tried your solution, but still it does not give the density (of each
component) versus time. It gives density versus distance for different
frames. This could be easily done by g_density with an .ndx file. I need to
have a plot of density-time for each of the components of the system.

Please help...




Best regards


On Wed, Apr 6, 2016 at 7:13 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi Faezeh,
>
> You can count the number of contacts within and between groups to follow
> the process over time using gmx mindist.
>
> Hope it helps,
>
> Tsjerk
> On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:
>
> > Hi Tsjerk,
> >
> > Thanks, but my question it is not that simple.
> > I am dealing with phase separation of a two-component system. At the end
> of
> > simulation the mixed system phase separate to two phases, one is rich in
> > one component and the other phase is rich with the other component. So I
> > want to see how each component  reachs those fractions by time?
> >
> >
> >
> > Best regards
> >
> >
> > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> > wrote:
> >
> > > Hi Faezeh,
> > >
> > > Using -b/-e flags you can get the density profile over a window of time
> > (or
> > > a single frame). Afterwards you can combine the results to have a
> density
> > > profile over time.
> > >
> > > Hope it helps,
> > >
> > > Tsjerk
> > >
> > > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Is it possible to obtain partial density versus time in Gromacs?
> > > Precisely,
> > > > I have a system of two components which separate by time. I need the
> > > > evolution of density of each phase by time?
> > > >
> > > > thanks.
> > > > Best regards
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Thanks alot  Negar!!

I am going to try, I'll ask you if I face with a problem.


Best regards


On Wed, Apr 6, 2016 at 5:09 PM, Negar Ashari Astani <negarast...@gmail.com>
wrote:

> ... Yes, I guess this can be easily done using Density profile tool of
> VMD. Since you are running classical simulations with gromacs you probably
> have your system topology with different residues and fragments. So you can
> easily choose each phase of your system in selected atoms (a combination of
> residues) and ask for the the density of this phase in the course of
> simulation. You just need to be careful when converting the units, as this
> plugin counts the atoms, thus if you have water molecule, the plugin counts
> that molecule three times (three atoms of the molecule), so you need to put
> "Name O and residue WAT" such that it counts a water molecule only once!
>
> Let me know if you need more explanation,
> Best,
> Negar
>
> On Wed, Apr 6, 2016 at 4:59 PM Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
>> Thanks Negar.
>>
>> More detail; my system phase-separate after equilibrium, such that each
>> component reaches two mole (or mass) fractions. One mole fraction at its
>> rich-phase and one mole fraction at its poor phase. I need to know those
>> two densities or fractions.
>>
>> I do not know your way.  Could you explain me a bit more.
>>
>>
>> Best regards
>>
>>
>> On Wed, Apr 6, 2016 at 4:45 PM, Negar Ashari Astani <
>> negarast...@gmail.com> wrote:
>>
>>>  Just a correction: The main plugin I used is " Density profile
>>> tool" and then for visualization as a volumetric density I used VOLMAP.
>>>
>>> On Wed, Apr 6, 2016 at 4:42 PM Negar Ashari Astani <
>>> negarast...@gmail.com> wrote:
>>>
>>>> Hello Faezeh,
>>>>
>>>> If by density you mean the mass density, you can use VOLMAP plugin of
>>>> VMD to analyze the density evolution in the course of simulation.
>>>> If this is what you mean, I'll be happy to help with more information.
>>>>
>>>> Best,
>>>> Negar
>>>>
>>>>
>>>> On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh <fpoosa...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Is it possible to obtain partial density versus time in Gromacs?
>>>>> Precisely,
>>>>> I have a system of two components which separate by time. I need the
>>>>> evolution of density of each phase by time?
>>>>>
>>>>> thanks.
>>>>> Best regards
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>>>
>>
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Hi Tsjerk,

Thanks, but my question it is not that simple.
I am dealing with phase separation of a two-component system. At the end of
simulation the mixed system phase separate to two phases, one is rich in
one component and the other phase is rich with the other component. So I
want to see how each component  reachs those fractions by time?



Best regards


On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hi Faezeh,
>
> Using -b/-e flags you can get the density profile over a window of time (or
> a single frame). Afterwards you can combine the results to have a density
> profile over time.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi,
> >
> > Is it possible to obtain partial density versus time in Gromacs?
> Precisely,
> > I have a system of two components which separate by time. I need the
> > evolution of density of each phase by time?
> >
> > thanks.
> > Best regards
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Partial density versus time

[Faezeh Pousaneh]

Thanks Negar.

More detail; my system phase-separate after equilibrium, such that each
component reaches two mole (or mass) fractions. One mole fraction at its
rich-phase and one mole fraction at its poor phase. I need to know those
two densities or fractions.

I do not know your way.  Could you explain me a bit more.


Best regards


On Wed, Apr 6, 2016 at 4:45 PM, Negar Ashari Astani <negarast...@gmail.com>
wrote:

>  Just a correction: The main plugin I used is " Density profile tool"
> and then for visualization as a volumetric density I used VOLMAP.
>
> On Wed, Apr 6, 2016 at 4:42 PM Negar Ashari Astani <negarast...@gmail.com>
> wrote:
>
>> Hello Faezeh,
>>
>> If by density you mean the mass density, you can use VOLMAP plugin of VMD
>> to analyze the density evolution in the course of simulation.
>> If this is what you mean, I'll be happy to help with more information.
>>
>> Best,
>> Negar
>>
>>
>> On Wed, Apr 6, 2016 at 4:30 PM Faezeh Pousaneh <fpoosa...@gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Is it possible to obtain partial density versus time in Gromacs?
>>> Precisely,
>>> I have a system of two components which separate by time. I need the
>>> evolution of density of each phase by time?
>>>
>>> thanks.
>>> Best regards
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
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[gmx-users] Partial density versus time

[Faezeh Pousaneh]

Hi,

Is it possible to obtain partial density versus time in Gromacs? Precisely,
I have a system of two components which separate by time. I need the
evolution of density of each phase by time?

thanks.
Best regards
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Re: [gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

To whom may have similar problem, that is how I solved it:

First of all, Gromacs by default uses center of mass removal (at least in
versions I use), but that is for 'whole system'. In my case I  have a
two-component system and I am interested in collecting density for one of
the components.
So, I used -fit obtain in trjconv to remove transnational movement of
component 2:

trjconv_mpi -fit translation -s production.tpr -f traj.xtc -o OUTPUT.xtc
chose component 2 and 2,

Then, I collect densities from produced OUTPUT.xtc.


Best regards


On Fri, Nov 13, 2015 at 1:38 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:

> Justin, thanks for comment.
> In fact I am going to analyze g_density, but I see center of mass moves. I
> have two-component system which has phase separated after a very long time.
> I can't redo the simulation.
> I could not mange that by tajconv.
> Can I take the final .gro file of current simulation and run it with COM
> removal to collect density?
>
>
> Best regards
>
>
> On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> Please some one help me how to remove center of mass motion in a
>>> trajectory
>>> which is already created without  this setting? is that possible?
>>>
>>>
>> Not using COM motion removal during the run leads to artifacts; no amount
>> of post-processing will fix that.  If you're just looking to re-center some
>> molecule(s) of interest, that's what trjconv is for.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>
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[gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

Hi,

Please some one help me how to remove center of mass motion in a trajectory
which is already created without  this setting? is that possible?

thanks in advance,

Best regards
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Re: [gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

Justin, thanks for comment.
In fact I am going to analyze g_density, but I see center of mass moves. I
have two-component system which has phase separated after a very long time.
I can't redo the simulation.
I could not mange that by tajconv.
Can I take the final .gro file of current simulation and run it with COM
removal to collect density?


Best regards


On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> Please some one help me how to remove center of mass motion in a
>> trajectory
>> which is already created without  this setting? is that possible?
>>
>>
> Not using COM motion removal during the run leads to artifacts; no amount
> of post-processing will fix that.  If you're just looking to re-center some
> molecule(s) of interest, that's what trjconv is for.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] cut-off

[Faezeh Pousaneh]

Thank you Justin,


Best regards


On Fri, Jun 19, 2015 at 2:40 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/18/15 7:47 AM, Faezeh Pousaneh wrote:

 Thanks Justin.

 yes, you are right, my simulation is very sensitive to cut-off.

 I did not understand what do you meant by '' is the balance of forces
 correct''?


 For this you should read about how force fields are derived.  Far too
 extensive of a topic for email, sorry.

  So If I understood you correctly, the cut-off lengths must be chosen from
 the force filed, yes?


 Yes.

  Since I am not expert how to choose a force field, could you tell me a
 proper force field for Benzene all-atom model?


 Try a few; see which one reproduces its physical properties best for
 whatever your intended purposes are.  No model perfectly captures
 everything.

 -Justin


 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] cut-off

[Faezeh Pousaneh]

Thanks Justin.

yes, you are right, my simulation is very sensitive to cut-off.

I did not understand what do you meant by '' is the balance of forces
correct''?

So If I understood you correctly, the cut-off lengths must be chosen from
the force filed, yes?
Since I am not expert how to choose a force field, could you tell me a
proper force field for Benzene all-atom model?

Best regards


On Thu, Jun 18, 2015 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/18/15 7:25 AM, Faezeh Pousaneh wrote:

 thanks David.
 but I am wondering for example if a chosen short cut-off produces correct
 experimental data, should I still make it larger or PME?


 Playing with cutoffs to try to force models to behave a certain way.  You
 might get a right answer, but is the balance of forces correct?  Force
 fields are generally tuned to be used with specific nonbonded regimes and
 shouldn't be altered unless systematic studies of those setups have been
 done.

  No that is an all-atom model.


 Just for pedantic sake, GROMOS96 54A7 is indeed a UA force field, but
 aromatic H are represented explicitly.  So in this case, the electrostatic
 treatment is indeed important.  PME makes the Coulombic cutoff a bit more
 flexible, but van der Waals interactions are going to be significant in a
 system like this and can be very sensitive to changes in the cutoff.

 -Justin



 Best regards


 On Wed, Jun 17, 2015 at 2:50 PM, David van der Spoel 
 sp...@xray.bmc.uu.se
 wrote:

  On 17/06/15 14:22, Faezeh Pousaneh wrote:

  Hi,

 Does the choice of cut-off length depends on the chosen force filed? or
 it
 can be chosen such that the simulation produces the experimental values?

  Cutoff should be used consistently, each force field has their setting,
 however that does not mean these settings are optimal.
 Here is a recent paper on organic liquids discussing this.
 http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00190



  In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for
 both LJ and coul interactions, is that fine?

  Is it united atom? In that case you have no Coulomb. However from our
 work
 above it follows that 1.2 nm is too short and for accurate results you
 need
 to use PME for both Coulomb and Van der Waals.


 thanks
 Best regards



 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell  Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
 sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
 --
 Gromacs Users mailing list

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 send a mail to gmx-users-requ...@gromacs.org.


 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

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Re: [gmx-users] cut-off

[Faezeh Pousaneh]

thanks David.
but I am wondering for example if a chosen short cut-off produces correct
experimental data, should I still make it larger or PME?

No that is an all-atom model.


Best regards


On Wed, Jun 17, 2015 at 2:50 PM, David van der Spoel sp...@xray.bmc.uu.se
wrote:

 On 17/06/15 14:22, Faezeh Pousaneh wrote:

 Hi,

 Does the choice of cut-off length depends on the chosen force filed? or it
 can be chosen such that the simulation produces the experimental values?

 Cutoff should be used consistently, each force field has their setting,
 however that does not mean these settings are optimal.
 Here is a recent paper on organic liquids discussing this.
 http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00190



 In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for
 both LJ and coul interactions, is that fine?

 Is it united atom? In that case you have no Coulomb. However from our work
 above it follows that 1.2 nm is too short and for accurate results you need
 to use PME for both Coulomb and Van der Waals.


 thanks
 Best regards



 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell  Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
 sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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 Gromacs Users mailing list

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Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Just for those who may face with similar problem as I had. I found where my
mistake was.

The problem: I have been obtaining Cv and Cp differently for Lutidine. The
obtained heat capacities in Groamcs were consistent with

kB T^2 c_P = Var (Enthalpy)
kB T^2 c_V = Var (Energy)

but not with

Cv = (dU/dT)_V

Cp = (dH/dT)_P.

Answer: The answer was for (dU/dT)_V I had simulated (NVT) at two
different temperatures and was obtaining energy derivatives, while the
volumes were different at two temperatures. Now I kept the volume the same
at two temperature and I get the same results as approach 1.

In fact there is a difference in Cv and Cp in my molecule, as it is seen in
the link for Benzene:

https://books.google.se/books?id=eH_1dIZr-zMCpg=PA171dq=liquid+benzene+Cp-Cvhl=ensa=Xved=0CB8Q6AEwAGoVChMIzoPJ0diWxgIVRI4sCh0wCwl0#v=onepageq=liquid%20benzene%20Cp-Cvf=false

Best regards


On Thu, Jun 11, 2015 at 8:10 PM, David van der Spoel sp...@xray.bmc.uu.se
wrote:

 On 09/06/15 17:29, Michael Shirts wrote:

 If the simulation are generating configurations with the Boltzmann
 probability distribution, the results should the same up to error.

 Cv and Cp should not be exactly the same, though for liquids at room
 temperature, they are pretty close (look up the precise numbers for the
 fluid you are interested in).

 This is not correct. cP and cV can easily differ 20-30%. Not many cV have
 been measured but you can compute the difference from other fluctuation
 formulae, see e.g. Caleman et al. J. Chem. Theory Comput. 2012, 8, 61–74,
 http://dx.doi.org/10.1021/ct200731v.
 Note that to get accurate numbers you need quantum corrections as well. My
 group are working on implementing a method for that in gmx dos.



 Are you calculating enthalpy as U + PV, where P is the constant APPLIED
 pressure, not the instantaneous pressure, and PV is in same units?  Since
 the PV term should be quite low for liquids, the two heat capacities
 should
 be relatively close (within noise -- fluctuation based calculations I
 think
 are noisier).

 Else you need to check if the Boltzmann distributions are being correctly
 generated: See the code and paper describing it linked here:
 https://github.com/shirtsgroup/checkensemble




 On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,

 Can I ask a question concerning your previous email,
 I followed

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 for my lutidine molecule, and I get same values for Cv and Cp. But when I
 test with

 kB T^2 c_P = Var (Enthalpy)
 kB T^2 c_V = Var (Energy)

 I get 40 J/mol.K difference in Cv and Cp.

 Mean that fluctuation play big role. Which way of checking I can rely?


 Best regards


 On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com
 wrote:

  By definition (more fundamental that fluctuation formulas)

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 Run two simulations at different T and estimate the derivatives.

 On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,

 I still would like to know what was your method you mentioned on last
 paragraph, just for learning:

 ''Also, to be sure, you should double check by calculating both heat
 capacities by finite difference formulas as well with two simulations

 at

 T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls

 don't

 agree within propagated error, then something is off.''

 ?
 thanks


 Best regards


 On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Andre,

 thank you for the link, you are probably right, It seems that my

 molecule

 has the difference Cp-Cv in the same range as benzene (since it has

 also

 ring structure).


 Best regards


 On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh 

 fpoosa...@gmail.com

 wrote:

  Dear Michael,

 I use  Parrinello-Rahman for barostat and v-rescale for thermostat.

 Sorry, could you explain more the second paragraph please? I did not

 get

 the method. What I checked so far is checking if gromacs correctly

 gives

 Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.




 Best regards


 On Mon, May 25, 2015 at 4:11 PM, Michael Shirts mrshi...@gmail.com


  wrote:

  Are you running with the Berendsen thermostat or barostat?  The

 gromacs

 g_energy functions for heat capacity use the fluctuation formula,

 and

 the

 fluctuations with both of these algorithms are wrong (as should be
 printed
 in the log file warning message). Make sure you use

 ensemble-preserving

 thermostats if you want fluctuation properties.

 Also, to be sure, you should double check by calculating both heat
 capacities by finite difference formulas as well with two

 simulations

 at

 T+dt/2 and T-dt/2 -- if the fluctuation and finite difference

 resutls

 don't
 agree within propagated error, then something is off.


 On Mon, May 25, 2015 at 5:59 AM, Faezeh Pousaneh 

 fpoosa...@gmail.com

 wrote:

  Hi,

 I do not know why I

[gmx-users] cut-off

[Faezeh Pousaneh]

Hi,

Does the choice of cut-off length depends on the chosen force filed? or it
can be chosen such that the simulation produces the experimental values?

In my case, I simulation Benzene with Gromos54A7 and I choose 1.2 nm for
both LJ and coul interactions, is that fine?

thanks
Best regards
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[gmx-users] compressibility

[Faezeh Pousaneh]

Hi,

I simulate a molecule in NPT ensemble, which I can not find any
experimental data about it's compressibility, what should I put in .mdp
file for it's compressibility in pressure coupling?

Best regards
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Re: [gmx-users] compressibility

[Faezeh Pousaneh]

Thank you Michael!


Best regards


On Fri, Jun 12, 2015 at 1:19 PM, Michael Shirts mrshi...@gmail.com wrote:

 The 'compressibility' in the pressure coupling is not actually the
 compressibility of the fluid; it's another way to write the mass of the
 fictitious piston.  It affects the inertia of the piston and the period of
 the oscillations of the box, but won't affect the magnitude of fluctuations
 of the box.  Having a value near the compressibility of the fluid, I
 believe, minimizes the chances of unstable simulations and weird
 resonances, but is not required.

 On Fri, Jun 12, 2015 at 3:12 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Hi,
 
  I simulate a molecule in NPT ensemble, which I can not find any
  experimental data about it's compressibility, what should I put in .mdp
  file for it's compressibility in pressure coupling?
 
  Best regards
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Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Dear Andre,

Many thanks for the message, was very useful. I followed your comments
carefully. Below;



 (1) I would suggest you not to take the last frame of the NPT simulation as
 the correct volume. You should instead take an average volume from the
 equilibrated NPT simulation and then edit the gro file to reach that
 average volume.


I tried this, but it did not help. The average volume is so close to the
last configuration volume.


 (2) are you sure that 10 ns is enough to properly sample heat capacities?
 Regarding this topic, I could ask you several questions:

 Actually not only 10 ns, but I have also tried a run up to 80 ns. I check
that all energy parameters are well equilibriated


 - Have you checked that all relevant structural and energetic patterns are
 fully relaxed within this time scale? For instance, energy components,
 density, radial distribution functions, relative orientation between
 molecules and so on.

 - Have you discarded the frames before structural and energetic relaxations
 were achieved?

 Yes, I have done.


 - Considering that lutidine is slightly bulky and has a well defined dipole
 moment, it may take a while for a full rotational relaxation. Have you
 computed the rotational correlation function to be sure that it relaxed
 long before 10 ns? If it did not relax, then 10 ns is not enough.

 - I like to compute these fluctuation-based properties as cumulative
 averages along the simulation (after structural and energetic relaxations,
 of course), it is easier to see if the average is approaching some plateau
 value (if not, longer simulation time is required).


That part I did not know, thanks for the comment. So I just checked them,
and I see the correlations also get equlibrated.



- I have never tested myself (has anyone tested?), but fluctuation-based
 calculations are obviously sensitive to the quality of the fluctuation, and
 double precision integration yields less noisier raw data than single
 precision integration does, so I would guess that double precision mdrun
 might provide a better-quality sampling of the fluctuation and would then
 improve the quality of your Cp and Cv estimates (just guessing).

 This also I just checked, but it does not improve that much.

As I already stated (and provided you published experimental data in
 support of my statement), Cp and Cv need not be the same for molecular
 liquids. But it is up to you to prove that your simulations are reliable
 (my questions above are just a fraction of the checks you need to perform
 in order to convince yourself and your audience that you have obtained
 reliable data and not just simulation artifacts). In principle, you should
 include these checks in the supporting information of your manuscripts to
 convince the editors and referees (and the general audience after
 publication) that you have been thorough in your investigation.

 Yes, I read the paper you gave and they can be different in some
molecules. But still you are right and I am not convinced about my
simulation yet. So I am trying to solve the problem. What I realized during
the checking is, when I change thermostat from V-rescale to Nose-hoover, I
get different results. Moreover, tau_t is also crucial in my simulation. I
had before 0.1, but when I change it to 0.2 I get a bigger C_v.


 best

 Andre

 On Wed, Jun 10, 2015 at 9:54 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,
 
  Could you please comment on my last question, thanks a lot.
  I have noticed that when I run both NVT and NPT simulations from a same
  .gro file (obtained from energy minimization) I obtain same Cv and Cp for
  two ensembles. However, so far I was running NVT after NPT (meaning I
 used
  .gro file obtained from NPT as initial configuration for NVT, since I
  wanted to have correct volume). The second way gives that big difference
 in
  Cv and Cp.
  I run a long simulations in all cases, but why both ways produce such
  difference?
 
 
 
  Best regards
 
 
  On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts mrshi...@gmail.com
 wrote:
 
   The variance formula is derived from the derivative formula + the
   assumption the distribution in Boltzmann, so they must agree if the
   distribution is Boltzmann.
  
   On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com
   wrote:
  
Thank you so much for the reply.
   
Yes, I use contact applied pressure and I am careful about units. I
   checked
and average enthalpy and U are close, meaning that PV is negligible.
  But
the point is variance of enthalpy in NPT differs from variance of
  energy
   in
NVT and that causes the difference.
   
You had given me an article showing that for example for Benzene the
difference in Cv and Cp is 25%, and here Ii get similar ( my molecule
  is
also carbon ring). But still I can answer why two both ways does not
  give
same Cv-Cp.
I will follow your suggestion.
   
   
   
Best regards

Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Dear Michael,

Could you please comment on my last question, thanks a lot.
I have noticed that when I run both NVT and NPT simulations from a same
.gro file (obtained from energy minimization) I obtain same Cv and Cp for
two ensembles. However, so far I was running NVT after NPT (meaning I used
.gro file obtained from NPT as initial configuration for NVT, since I
wanted to have correct volume). The second way gives that big difference in
Cv and Cp.
I run a long simulations in all cases, but why both ways produce such
difference?



Best regards


On Tue, Jun 9, 2015 at 5:45 PM, Michael Shirts mrshi...@gmail.com wrote:

 The variance formula is derived from the derivative formula + the
 assumption the distribution in Boltzmann, so they must agree if the
 distribution is Boltzmann.

 On Tue, Jun 9, 2015 at 11:43 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Thank you so much for the reply.
 
  Yes, I use contact applied pressure and I am careful about units. I
 checked
  and average enthalpy and U are close, meaning that PV is negligible. But
  the point is variance of enthalpy in NPT differs from variance of energy
 in
  NVT and that causes the difference.
 
  You had given me an article showing that for example for Benzene the
  difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is
  also carbon ring). But still I can answer why two both ways does not give
  same Cv-Cp.
  I will follow your suggestion.
 
 
 
  Best regards
 
 
  On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts mrshi...@gmail.com
 wrote:
 
   If the simulation are generating configurations with the Boltzmann
   probability distribution, the results should the same up to error.
  
   Cv and Cp should not be exactly the same, though for liquids at room
   temperature, they are pretty close (look up the precise numbers for the
   fluid you are interested in).
  
   Are you calculating enthalpy as U + PV, where P is the constant APPLIED
   pressure, not the instantaneous pressure, and PV is in same units?
 Since
   the PV term should be quite low for liquids, the two heat capacities
  should
   be relatively close (within noise -- fluctuation based calculations I
  think
   are noisier).
  
   Else you need to check if the Boltzmann distributions are being
 correctly
   generated: See the code and paper describing it linked here:
   https://github.com/shirtsgroup/checkensemble
  
  
  
  
   On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com
   wrote:
  
Dear Michael,
   
Can I ask a question concerning your previous email,
I followed
   
Cv = (dU/dT)_V
   
Cp = (dH/dT)_P
   
for my lutidine molecule, and I get same values for Cv and Cp. But
  when I
test with
   
kB T^2 c_P = Var (Enthalpy)
kB T^2 c_V = Var (Energy)
   
I get 40 J/mol.K difference in Cv and Cp.
   
Mean that fluctuation play big role. Which way of checking I can
 rely?
   
   
Best regards
   
   
On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com
wrote:
   
 By definition (more fundamental that fluctuation formulas)

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 Run two simulations at different T and estimate the derivatives.

 On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh 
  fpoosa...@gmail.com
 wrote:

  Dear Michael,
 
  I still would like to know what was your method you mentioned on
  last
  paragraph, just for learning:
 
  ''Also, to be sure, you should double check by calculating both
  heat
  capacities by finite difference formulas as well with two
  simulations
at
  T+dt/2 and T-dt/2 -- if the fluctuation and finite difference
  resutls
 don't
  agree within propagated error, then something is off.''
 
  ?
  thanks
 
 
  Best regards
 
 
  On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh 
   fpoosa...@gmail.com
  wrote:
 
   Dear Andre,
  
   thank you for the link, you are probably right, It seems that
 my
 molecule
   has the difference Cp-Cv in the same range as benzene (since it
  has
 also
   ring structure).
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh 
fpoosa...@gmail.com
   wrote:
  
   Dear Michael,
  
   I use  Parrinello-Rahman for barostat and v-rescale for
   thermostat.
  
   Sorry, could you explain more the second paragraph please? I
 did
   not
 get
   the method. What I checked so far is checking if gromacs
  correctly
 gives
   Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it
 gives.
  
  
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:11 PM, Michael Shirts 
   mrshi...@gmail.com

   wrote:
  
   Are you running with the Berendsen thermostat or barostat?
 The
 gromacs
   g_energy functions for heat capacity

Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Dear Michael,

Can I ask a question concerning your previous email,
I followed

Cv = (dU/dT)_V

Cp = (dH/dT)_P

for my lutidine molecule, and I get same values for Cv and Cp. But when I
test with

kB T^2 c_P = Var (Enthalpy)
kB T^2 c_V = Var (Energy)

I get 40 J/mol.K difference in Cv and Cp.

Mean that fluctuation play big role. Which way of checking I can rely?


Best regards


On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com wrote:

 By definition (more fundamental that fluctuation formulas)

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 Run two simulations at different T and estimate the derivatives.

 On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,
 
  I still would like to know what was your method you mentioned on last
  paragraph, just for learning:
 
  ''Also, to be sure, you should double check by calculating both heat
  capacities by finite difference formulas as well with two simulations at
  T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls
 don't
  agree within propagated error, then something is off.''
 
  ?
  thanks
 
 
  Best regards
 
 
  On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh fpoosa...@gmail.com
  wrote:
 
   Dear Andre,
  
   thank you for the link, you are probably right, It seems that my
 molecule
   has the difference Cp-Cv in the same range as benzene (since it has
 also
   ring structure).
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh fpoosa...@gmail.com
   wrote:
  
   Dear Michael,
  
   I use  Parrinello-Rahman for barostat and v-rescale for thermostat.
  
   Sorry, could you explain more the second paragraph please? I did not
 get
   the method. What I checked so far is checking if gromacs correctly
 gives
   Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.
  
  
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:11 PM, Michael Shirts mrshi...@gmail.com
   wrote:
  
   Are you running with the Berendsen thermostat or barostat?  The
 gromacs
   g_energy functions for heat capacity use the fluctuation formula, and
  the
   fluctuations with both of these algorithms are wrong (as should be
   printed
   in the log file warning message). Make sure you use
 ensemble-preserving
   thermostats if you want fluctuation properties.
  
   Also, to be sure, you should double check by calculating both heat
   capacities by finite difference formulas as well with two simulations
  at
   T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls
   don't
   agree within propagated error, then something is off.
  
  
   On Mon, May 25, 2015 at 5:59 AM, Faezeh Pousaneh 
 fpoosa...@gmail.com
   wrote:
  
Hi,
   
I do not know why I obtain two difference cp and cv from NVT and
 NPT
simulations.
What I do is, I take 1000 lutidne molecules, and I do firstly an
  energy
minimization with steep integrator, then NPT simulation at T=300
 and
   P=1
atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with
 same
   mdp
file except no pressure coupling, and with initial .gro file
 obtained
   from
NPT run, (I obtain Cv=180).
Does some one know where is my mistake? (In both runs, I obtain Cv
  and
   Cp
from g_energy and in different time intervals and after
 equilibrited
   time)
   
   
Best regards
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Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

The latter way, I meant in NPT and NVT simulation respectively. I noted
that Gromacs produces Cv and Cp from the latter case.


Best regards


On Tue, Jun 9, 2015 at 5:23 PM, Faezeh Pousaneh fpoosa...@gmail.com wrote:

 Dear Michael,

 Can I ask a question concerning your previous email,
 I followed

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 for my lutidine molecule, and I get same values for Cv and Cp. But when I
 test with

 kB T^2 c_P = Var (Enthalpy)
 kB T^2 c_V = Var (Energy)

 I get 40 J/mol.K difference in Cv and Cp.

 Mean that fluctuation play big role. Which way of checking I can rely?


 Best regards


 On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com
 wrote:

 By definition (more fundamental that fluctuation formulas)

 Cv = (dU/dT)_V

 Cp = (dH/dT)_P

 Run two simulations at different T and estimate the derivatives.

 On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,
 
  I still would like to know what was your method you mentioned on last
  paragraph, just for learning:
 
  ''Also, to be sure, you should double check by calculating both heat
  capacities by finite difference formulas as well with two simulations at
  T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls
 don't
  agree within propagated error, then something is off.''
 
  ?
  thanks
 
 
  Best regards
 
 
  On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh fpoosa...@gmail.com
  wrote:
 
   Dear Andre,
  
   thank you for the link, you are probably right, It seems that my
 molecule
   has the difference Cp-Cv in the same range as benzene (since it has
 also
   ring structure).
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh fpoosa...@gmail.com
 
   wrote:
  
   Dear Michael,
  
   I use  Parrinello-Rahman for barostat and v-rescale for thermostat.
  
   Sorry, could you explain more the second paragraph please? I did not
 get
   the method. What I checked so far is checking if gromacs correctly
 gives
   Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.
  
  
  
  
   Best regards
  
  
   On Mon, May 25, 2015 at 4:11 PM, Michael Shirts mrshi...@gmail.com
   wrote:
  
   Are you running with the Berendsen thermostat or barostat?  The
 gromacs
   g_energy functions for heat capacity use the fluctuation formula,
 and
  the
   fluctuations with both of these algorithms are wrong (as should be
   printed
   in the log file warning message). Make sure you use
 ensemble-preserving
   thermostats if you want fluctuation properties.
  
   Also, to be sure, you should double check by calculating both heat
   capacities by finite difference formulas as well with two
 simulations
  at
   T+dt/2 and T-dt/2 -- if the fluctuation and finite difference
 resutls
   don't
   agree within propagated error, then something is off.
  
  
   On Mon, May 25, 2015 at 5:59 AM, Faezeh Pousaneh 
 fpoosa...@gmail.com
   wrote:
  
Hi,
   
I do not know why I obtain two difference cp and cv from NVT and
 NPT
simulations.
What I do is, I take 1000 lutidne molecules, and I do firstly an
  energy
minimization with steep integrator, then NPT simulation at T=300
 and
   P=1
atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with
 same
   mdp
file except no pressure coupling, and with initial .gro file
 obtained
   from
NPT run, (I obtain Cv=180).
Does some one know where is my mistake? (In both runs, I obtain Cv
  and
   Cp
from g_energy and in different time intervals and after
 equilibrited
   time)
   
   
Best regards
--
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 before
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Re: [gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Thank you so much for the reply.

Yes, I use contact applied pressure and I am careful about units. I checked
and average enthalpy and U are close, meaning that PV is negligible. But
the point is variance of enthalpy in NPT differs from variance of energy in
NVT and that causes the difference.

You had given me an article showing that for example for Benzene the
difference in Cv and Cp is 25%, and here Ii get similar ( my molecule is
also carbon ring). But still I can answer why two both ways does not give
same Cv-Cp.
I will follow your suggestion.



Best regards


On Tue, Jun 9, 2015 at 5:29 PM, Michael Shirts mrshi...@gmail.com wrote:

 If the simulation are generating configurations with the Boltzmann
 probability distribution, the results should the same up to error.

 Cv and Cp should not be exactly the same, though for liquids at room
 temperature, they are pretty close (look up the precise numbers for the
 fluid you are interested in).

 Are you calculating enthalpy as U + PV, where P is the constant APPLIED
 pressure, not the instantaneous pressure, and PV is in same units?  Since
 the PV term should be quite low for liquids, the two heat capacities should
 be relatively close (within noise -- fluctuation based calculations I think
 are noisier).

 Else you need to check if the Boltzmann distributions are being correctly
 generated: See the code and paper describing it linked here:
 https://github.com/shirtsgroup/checkensemble




 On Tue, Jun 9, 2015 at 11:23 AM, Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Dear Michael,
 
  Can I ask a question concerning your previous email,
  I followed
 
  Cv = (dU/dT)_V
 
  Cp = (dH/dT)_P
 
  for my lutidine molecule, and I get same values for Cv and Cp. But when I
  test with
 
  kB T^2 c_P = Var (Enthalpy)
  kB T^2 c_V = Var (Energy)
 
  I get 40 J/mol.K difference in Cv and Cp.
 
  Mean that fluctuation play big role. Which way of checking I can rely?
 
 
  Best regards
 
 
  On Tue, May 26, 2015 at 3:38 PM, Michael Shirts mrshi...@gmail.com
  wrote:
 
   By definition (more fundamental that fluctuation formulas)
  
   Cv = (dU/dT)_V
  
   Cp = (dH/dT)_P
  
   Run two simulations at different T and estimate the derivatives.
  
   On Tue, May 26, 2015 at 5:12 AM, Faezeh Pousaneh fpoosa...@gmail.com
   wrote:
  
Dear Michael,
   
I still would like to know what was your method you mentioned on last
paragraph, just for learning:
   
''Also, to be sure, you should double check by calculating both heat
capacities by finite difference formulas as well with two simulations
  at
T+dt/2 and T-dt/2 -- if the fluctuation and finite difference resutls
   don't
agree within propagated error, then something is off.''
   
?
thanks
   
   
Best regards
   
   
On Mon, May 25, 2015 at 5:10 PM, Faezeh Pousaneh 
 fpoosa...@gmail.com
wrote:
   
 Dear Andre,

 thank you for the link, you are probably right, It seems that my
   molecule
 has the difference Cp-Cv in the same range as benzene (since it has
   also
 ring structure).


 Best regards


 On Mon, May 25, 2015 at 4:44 PM, Faezeh Pousaneh 
  fpoosa...@gmail.com
 wrote:

 Dear Michael,

 I use  Parrinello-Rahman for barostat and v-rescale for
 thermostat.

 Sorry, could you explain more the second paragraph please? I did
 not
   get
 the method. What I checked so far is checking if gromacs correctly
   gives
 Cv,Cp= Var(Energy or Enthalpy)/kBT^2 , and I find that it gives.




 Best regards


 On Mon, May 25, 2015 at 4:11 PM, Michael Shirts 
 mrshi...@gmail.com
  
 wrote:

 Are you running with the Berendsen thermostat or barostat?  The
   gromacs
 g_energy functions for heat capacity use the fluctuation formula,
  and
the
 fluctuations with both of these algorithms are wrong (as should
 be
 printed
 in the log file warning message). Make sure you use
   ensemble-preserving
 thermostats if you want fluctuation properties.

 Also, to be sure, you should double check by calculating both
 heat
 capacities by finite difference formulas as well with two
  simulations
at
 T+dt/2 and T-dt/2 -- if the fluctuation and finite difference
  resutls
 don't
 agree within propagated error, then something is off.


 On Mon, May 25, 2015 at 5:59 AM, Faezeh Pousaneh 
   fpoosa...@gmail.com
 wrote:

  Hi,
 
  I do not know why I obtain two difference cp and cv from NVT
 and
   NPT
  simulations.
  What I do is, I take 1000 lutidne molecules, and I do firstly
 an
energy
  minimization with steep integrator, then NPT simulation at
 T=300
   and
 P=1
  atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with
   same
 mdp
  file except no pressure coupling, and with initial .gro file
   obtained
 from
  NPT run, (I obtain Cv=180).
  Does

[gmx-users] g_covar

[Faezeh Pousaneh]

Hi,

I need help please.
I am calculating entropy of a single water in water solution. So I did a 10
ns NPT. Then I run

g_covar -f NPT.xtc -s NPT.tpr  -o  -l   -av   -v

and

g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg


I have two questions.

1- In the g_covar it asks to select group,  should I choose 'system'
for both asks, or choose a 'single water'?

2- When I choose different time frames (of course after equilibrium), I get
completely different entropy, why is that so?

Best regards
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[gmx-users] energy between different groups

[Faezeh Pousaneh]

Hi,

I simulate liquid water 1397 molecules with specifying two groups with
index file; 1 molecule and rest of the molecules 1396. When I obtain
average LJ energy per molecule for whole system (with -nmol), I get  16
kJ/mol, but when I obtain it from interaction between groups,
 LJ-SR:group1-group2, I get 8  kJ/mol. A factor of 2 is missing. Can any
one who knows please explain me why?

thank you
Best regards
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[gmx-users] entropy of water

[Faezeh Pousaneh]

Hi,

I need help please.
I am calculating entropy of a single water in water solution. So I did a 10
ns with output  NPT. Then I run

g_covar -f NPT.xtc -s NPT.tpr  -o  -l   -av   -v

and

g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg


I have two questions.

1- In the g_covar it asks to select group,  should I choose system for both
aks?

2- When I choose different time frames (of course after equilibrium), I get
completely different entropy, why is that so?



Best regards
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[gmx-users] number of Nodes after extension

[Faezeh Pousaneh]

Hi,

A question please,
Can I change the number of nodes for the extension of the first run (let us
say first run was with 10 nodes and now I want to increase it to 20 in the
extension)? does that influence on the analysis of the runs?

thanks.
Best regards
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Re: [gmx-users] number of Nodes after extension

[Faezeh Pousaneh]

Thanks Mark!


Best regards


On Fri, May 29, 2015 at 10:19 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Yes you can do that. No, it doesn't matter.

 Mark

 On Fri, May 29, 2015 at 10:16 AM Faezeh Pousaneh fpoosa...@gmail.com
 wrote:

  Hi,
 
  A question please,
  Can I change the number of nodes for the extension of the first run (let
 us
  say first run was with 10 nodes and now I want to increase it to 20 in
 the
  extension)? does that influence on the analysis of the runs?
 
  thanks.
  Best regards
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[gmx-users] Different Cv and Cp

[Faezeh Pousaneh]

Hi,

I do not know why I obtain two difference cp and cv from NVT and NPT
simulations.
What I do is, I take 1000 lutidne molecules, and I do firstly an energy
minimization with steep integrator, then NPT simulation at T=300 and P=1
atm for 10ns, (I obtain Cp= 230), then I run NVT for 10 ns with same mdp
file except no pressure coupling, and with initial .gro file obtained from
NPT run, (I obtain Cv=180).
Does some one know where is my mistake? (In both runs, I obtain Cv and Cp
from g_energy and in different time intervals and after equilibrited time)


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