Dear Andre,<br><br>Thanks for the helpful information. <br><br>I need to do some text reading to understand the periodic BC effect you are talking about. I dont see why increasing length in z direction does not lead to periodic BC in z and only for x, y ? does that mean the thickness of layer would be the Z dimension? then how much increase in one direction is reasonable? (If I have a 2 nm box).<br>
<br>Also Can you please introduce some text book?<br><br>Thank you,<br>Best regards,<br><br><div class="gmail_quote">2011/3/15 André Farias de Moura <span dir="ltr"><<a href="mailto:moura@ufscar.br">moura@ufscar.br</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear Elisabeth,<br>
<br>
actually, it is the other way around, you need increase the box length in<br>
one direction, thus keeping periodic boundary conditions in the other two<br>
directions while a (infinitely periodic) surface is created. and notice that<br>
using genconf with -nbox 3 3 1 will increase your system but will not make<br>
it a surface system, unless you increase the box length in one direction.<br>
<br>
as regards the size, the larger the model system, the smaller should be<br>
the fluctuations. but mind that you should increase the size by a few<br>
order of magnitude for any noticeable decrease on the (huge) RMSD<br>
values you are getting. if you want to check the results for convergence<br>
maybe you could try either a block averaging or a running average (grace<br>
can do that for you).<br>
<br>
best regards<br>
<br>
Andre<br>
<div><div></div><div class="h5"><br>
On Mon, Mar 14, 2011 at 7:57 PM, Elisabeth <<a href="mailto:katesedate@gmail.com">katesedate@gmail.com</a>> wrote:<br>
> Hello,<br>
><br>
> Thank you for your answer.<br>
><br>
> 1- If I am right I have to increase the length in two directions rather than<br>
> one, to create a plane parallel to XY for example?<br>
><br>
> 2- Can you please give me an idea on how many molecules I need to have in<br>
> the box and also what should be the thickness of layer? I have now 3nm X 9 X<br>
> 9 dimensions. That is thickness of 3nm. What I did was replicating a 3nm box<br>
> using genconf -nbox 3 3 1. I dont know what is the correct way of creating a<br>
> layer for surface tension calculation.<br>
><br>
> I appreciate any comments about number of molecules, box dimensions for such<br>
> a study.<br>
><br>
> 3- my last question is how can I make sure surface tension reported by<br>
> g_energy is the equilibrated one. RMSD is very big compared to surf. ten. !<br>
><br>
> Thanks for your time.<br>
> Elisabeth<br>
><br>
> ******************************************<br>
><br>
> if you are interested in the surface tension of a pure liquid, which I<br>
> assume is<br>
> true from your message, then you need to create at least one surface, since<br>
> periodic boundary conditions make the model system infinite, i.e., without a<br>
> surface whatsoever.<br>
><br>
> the easiest way to make that happen is to increase the length of the box in<br>
> one direction, say the z direction. that way you will end up with a system<br>
> that<br>
> resemble a (thin) liquid film with vacuum below and above, meaning that you<br>
> now have two surfaces. run a regular simulation (NVT) e use g_energy to get<br>
> the surface tension.<br>
><br>
> btw: as any other pressure related property, fluctuations are huge.<br>
><br>
> best<br>
><br>
> Andre<br>
><br>
> On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth <<a href="mailto:katesedate@gmail.com">katesedate@gmail.com</a>> wrote:<br>
>> Dear gmx users,<br>
>><br>
>> Since I am new to surface tension topic I need to ask very trivial<br>
>> questions. Please help me out with these simple questions.<br>
>><br>
>> As a starting point I am going to calculate surface tension of a pure<br>
>> alkane<br>
>> in a cubic box and compare with experimental values.<br>
>><br>
>> 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface<br>
>> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e<br>
>> Pres-XX-(bar), Pres-YY(bar), Pres--(bar)<br>
>><br>
>> Can anyone tell me what the difference between these two is?<br>
>><br>
>> 2- In pressure coupling settings there is surface_tension option which I<br>
>> guess is applicable where surface tension needs to be kept fixed. If one<br>
>> want to calculate surface tension I dont think this option make sense. Am<br>
>> I<br>
>> right?<br>
>><br>
>> 3- I am using the following setting: I calculate the average for a 2ns run<br>
>> and different start times as shown below. Although T, P and other<br>
>> quantities<br>
>> are equilibrated after 200ps, surface tension is not giving a constant<br>
>> value. Is that because I am not using berenden P coupling? (As mentioned<br>
>> in<br>
>> the manual surface tension works with berendsen)<br>
>><br>
>> Pcoupl = Parrinello-Rahman<br>
>> Pcoupltype = isotropic<br>
>> tau_p = 1 1<br>
>> compressibility = 4.5e-5<br>
>> ref_p = 40<br>
>><br>
>><br>
>> time period for which average is calculated Average RMSD<br>
>> Fluct. Drift Tot-Drift<br>
>><br>
>> -------------------------------------------------------------------------------<br>
>> 1-2000 ps run: #Surf*SurfTen 6.43844 3588.74<br>
>> 3588.35 0.091406 182.721<br>
>> 500-2000 ps #Surf*SurfTen 12.8518 3605.72<br>
>> 3605.26 0.132126 198.189<br>
>> 1000-2000ps #Surf*SurfTen 18.8821 3610.97<br>
>> 3610.8 0.11819 118.191<br>
>> 1500-2000ps #Surf*SurfTen 23.0072 3585.51<br>
>> 3584.93 -0.444037 -222.019<br>
>><br>
>><br>
>><br>
>> 4- Assuming I am getting surface tension for a cubic box, to compare this<br>
>> with reported values in literature I need to divide by 6 (no. of<br>
>> surfaces)?<br>
>><br>
>> 5- Does box six affect the results? (mine is 3.3 nm ).<br>
>><br>
>><br>
>> Thank you,<br>
>><br>
</div></div></blockquote></div><br>