[gmx-users] Thin film drifting

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 30 08:46:17 CEST 2020 

Den 2020-03-29 kl. 22:46, skrev Alex:
> On Sun, Mar 29, 2020 at 2:49 PM David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> 
>> Den 2020-03-29 kl. 19:43, skrev Alex:
>>> Thanks.
>>>
>>> On Sun, Mar 29, 2020 at 11:59 AM David van der Spoel <
>> spoel at xray.bmc.uu.se>
>>> wrote:
>>>
>>>> Den 2020-03-29 kl. 15:16, skrev Alex:
>>>>> Thank Prof. van der Spoel for the response.
>>>>> No, it isn't. The thin film is solid. There are interaction within the
>>>> thin
>>>>> film and with water in the interface.
>>>>>
>>>>> Please find a short movie of the unwrapped trajectory of the simulation
>>>> in
>>>>> below link (water molecules are hidden); It shows minimization, then
>>>>> equalization (NVT : tcoupl = v-rescale), then equalization (NpT :
>> tcoupl
>>>> =
>>>>> v-rescale and pcoupl = berendsen) and then production (NpT : tcoupl =
>>>>> v-rescale and pcoupl = Parrinello-Rahman).
>>>>>
>>>>> https://drive.google.com/open?id=1jk-Pun1BICNArGJaW0ydIY5TTivECGMf
>>>>>
>>>>> The thin film starts drifting significantly in the production along
>> both
>>>> x
>>>>> and y directions.
>>>> Thanks, do you have isotropic pressure scaling?
>>>>
>>> Yes, the pcoupltype is isotropic. Please find the mdp file in below link.
>>> https://drive.google.com/open?id=1iYt6eTcQ4SBi1A9ZFOenL7Q7wc37UvLa
>>>
>>>>
>>>> Is the shift towards higher x and y values?
>>>>
>>> The shift is toward higher y value (+y).
>>> It also firstly goes toward higher x value (+x ) for a very short time
>> and
>>> then switches the direction to toward lower x value (-x) and finally
>> shifts
>>> toward lower x value (-x).
>>>
>> But how is the solid modeled? Are there covalent bonds? It is not
>> certain there is a problem, at least I am not convinced. In P scaling
>> the coordinates of all particles are scaled by a constant and then
>> certain atoms can hop over PBC. If you plot the center of mass including
>> periodic boundaries (i.e. without unwrapping) it will be nicely in the
>> center of the box with few fluctuations. gmx traj may do this for you.
>>
> The thin film contains 1075 epoxy molecules in which there is no
> inter-molecule covalent bond.
> Below are the COM of the thin film with and without pbc in gmx traj.
> 
> I admit you are right and the comm-grps works fine as gmx traj -pbc yes
> shows, thanks.
> PBC : Yes
> https://drive.google.com/open?id=14DRIZVt99x8SfO6qlkhPAeTkb7RQhsUp
> 
> PBC: No
> https://drive.google.com/open?id=1uWRgTATW9hUEOaQQnQozklUvux8psrPx
Note that the net movement is a lot smaller than the fluctuations in the 
in the one with PBC, I don't think there is any problem.

> 
>>
>> I and many others have done PMFs of small compounds over membranes of
>> different types, but not sure that anyone has noticed problems with
>> moving membranes.
> 
> I would also be so appreciated if you give me your preferences of the
> following two choices I have in the PMF calculation of Mol_A to the
> thin-film.
> “comm-grps = *thin_film* *Mol_A* *SOL*”
> or
> “comm-grps = *Other* *SOL*”
> Where the Other group contains the thin film and molecule A.
> 

I would go for comm-grps = system.
Make sure to compute the pmf based on the relative distance between your 
compound and the membrane.

> Best regards,
> Alex
> 
>>
>>
>>> Maybe you can open an issue here:
>>>> https://gitlab.com/gromacs/gromacs/-/issues
>>>
>>> I will open an issue.
>>>
>>> Actually, in the later steps of the simulations, using umbrella sampling
>>> and wham, I want to simulate the PMF a single molecule (called A; 26
>> atoms)
>>> when it comes from water and diffuses inside the thin film till mid (com)
>>> of thin film. pull_group1 and pull_group2 would be the Mol_A and
>> thin_film,
>>> respectively.
>>>
>>> I don't know if this kind of drifting would affect on the PMF, if so,
>> how?
>>> If the comm-grps works I have the two following options to consider:
>>> “comm-grps = thin_film Mol_A SOL”
>>> or
>>> “comm-grps = Other SOL”
>>> Where the Other group contains the thin film and molecule A.
>>> Which one do you recommend, please?
>>>
>>> Thank you,
>>> Alex
>>>
>>>>
>>>>>
>>>>> Best regards,
>>>>> Alex
>>>>>
>>>>> On Sun, Mar 29, 2020 at 2:44 AM David van der Spoel <
>>>> spoel at xray.bmc.uu.se>
>>>>> wrote:
>>>>>
>>>>>> Den 2020-03-29 kl. 05:24, skrev Alex:
>>>>>>> Dear all,
>>>>>>> In a system, I have a thin_film (infinitive in x-y directions) with
>>>> water
>>>>>>> on top and bottom of it, PBC = xyz.
>>>>>>> By the below flags I try to remove the motion of the center of mass
>> of
>>>>>> the
>>>>>>> two group separately.
>>>>>>> comm-grps     = thin_film Water
>>>>>>> comm-mode   = Linear
>>>>>>> nstcomm         = 100
>>>>>>>
>>>>>>> However the thin film drift specially in x and y directions whereas I
>>>> was
>>>>>>> expecting to have no drifting for the thin film, If I understood
>>>>>> correctly
>>>>>>> the usage of the comm-grps!
>>>>>>>
>>>>>>> Would you please let me know how I can stop drifting of the thin
>> film?
>>>>>>>
>>>>>>> Thank you,
>>>>>>> Alex
>>>>>>>
>>>>>> Is that a liquid film? Are there interactions within the film and with
>>>>>> water? The comm removal will calculate the center of mass taking
>>>>>> periodic boundaries into account so if your film moves one molecule
>> at a
>>>>>> time the COM will stay in place. In a realistic system the friction
>>>>>> between water and film should prevent this, hav eyou tried turning off
>>>>>> comm?
>>>>>>
>>>>>> Historically this has been a fix for the Berendsen thermostat that
>>>>>> accumulates energy, however with a stochastic thermostat it should not
>>>>>> be necessary. Not sure about Nose-Hoover though.
>>>>>> --
>>>>>> 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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>>>>
>>>>
>>>> --
>>>> 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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>>
>>
>> --
>> 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
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>> posting!
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-- 
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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