Hi all<br><br>Can anyone help me out with the wall settings for running above mentioned liquid-liquid interface. with the mdp file i have my system is exploding. any help is highly appreciated.<br><br>Regards<br>Vinoth<br>
<br><div class="gmail_quote">On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan <span dir="ltr"><<a href="mailto:kmvinoth@gmail.com">kmvinoth@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Berk<br><br>Thank you. what settings i should change in mdp file (energy minimisation) to run the energy minimisation for the single liquid-liquid interface (liquid-vapour interface at the other two extremes) without any issues? kindly be specific ( what parameter i should change) below is my mdp file. any help is highly appreciated.<div>
<div></div><div class="h5"><br>
<br>integrator = steep <br>emtol = 40.0 <br>emstep = 0.01<br>nsteps = 10000 <br>nstxout = 100 <br>nstvout = 100 <br>nstfout = 100 <br>nstlog = 100 <br>
nstenergy = 100 <br>nstlist = 5 <br>ns_type = grid <br>rlist = 1.0 <br>coulombtype = PME <br>rcoulomb = 1.0 <br>vdwtype = Cut-off <br>rvdw = 1.0 <br>
ewald_geometry = 3dc<br>nwall = 2<br>wall_type = 9-3<br>wall_r_linpot = 1<br>wall_atomtype = opls_966 opls_968<br>wall_density = 9-3 9-3<br>wall_ewald_zfac = 3<br>pbc = xy <br>fourierspacing = 0.18 <br>
<br>Regards<br>Vinoth <br><br></div></div><div class="gmail_quote"><div><div></div><div class="h5">On Tue, Nov 2, 2010 at 3:41 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<div>
I meant to say that if you see effects of one interface on another with a layer of 1 nm thickness/height,<br>these effects will be less with a layer of 2 nm thickness and even less with 10 nm thickness.<br><br>Berk<br><br>
<hr>Date: Tue, 2 Nov 2010 15:30:34 +0530<div><div></div><div><br>Subject: Re: [gmx-users] Reg:walls and pbc xy<br>From: <a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<br>Hi Berk<br><br>Thank you once again. How can i use thick layers and what is the procedure? can you explain it bit more on this?<br><br>Regards<br>Vinoth<br><br><div>On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="padding-left: 1ex;">
<div>
Hi,<br><br>I have not heard about such issues, but it might depend a lot on your particular application.<br>I would think you will always have disturbances, no matter if you use two interfaces,<br>one interface with walls or one liquid-liquid interface and two liquid-vapour interfaces.<br>
The only solution to such problems is using thicker layers.<br><br>The wall are on the bottom (z=0) and top (z=z_box) of the box, as the manual says.<br><br>Berk<br><br><hr>Date: Tue, 2 Nov 2010 14:59:31 +0530<br>Subject: Re: [gmx-users] Reg:walls and pbc xy<div>
<div></div><div><br>From: <a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br>Hi Berk<br><br>
I need only one interface because if i have two interfaces the "capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off" (this was said in the literature).<br>
<br>Can anyone explain me why walls are used for interfaces? and what is the purpose of using walls?. <br>suppose if i put nwall =2 where exactly are the walls created? can anyone explain me with an example?<br><br>i read the manual but it is not making any sense to me. if i know this i know what correction i should make in my mdp file to make it work for pbc xy. any help is highly appreciated.<br>
<br>Regards<br>Vinoth<br><br><div>On Tue, Nov 2, 2010 at 1:37 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br><blockquote style="padding-left: 1ex;">
<div>
Hi,<br><br>With wall_r_linpot your wall potential is linear from 1 nm downwards.<br>Since the LJ force is negative at 1 nm, your atoms are attracted to the walls.<br><br>But why not simply use two interfaces? You get double the sampling for free<br>
and you do not have to bother with complicated wall setups.<br><br>Berk<br><br><hr>Date: Tue, 2 Nov 2010 11:49:48 +0530<br>From: <a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Reg:walls and pbc xy<div><div></div><div><br><br>Hi Gromacians<br><br>I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy direction and using walls. ( If i apply pbc in all the directions i get two interfaces where as i need only one interface hence i am applying it only on the xy direction and removing the boundary condition in the Z direction.).When i performed the energy minimisation for the interfacial system but i found that my system is exploding (several PDB files are written while running mdrun is executed) and i dont know why?.There is no issue when i use pbc in all directions. below is my em.mdp file. any help is highly appreciated.<br>
<br>integrator = steep <br>emtol = 40.0 <br>emstep = 0.01<br>nsteps = 10000 <br>nstxout = 100 <br>nstvout = 100 <br>nstfout = 100 <br>nstlog = 100 <br>
nstenergy = 100 <br>nstlist = 5 <br>ns_type = grid <br>rlist = 1.0 <br>coulombtype = PME <br>rcoulomb = 1.0 <br>vdwtype = Cut-off <br>rvdw = 1.0 <br>
ewald_geometry = 3dc<br>nwall = 2<br>wall_type = 9-3<br>wall_r_linpot = 1<br>wall_atomtype = opls_966 opls_968<br>wall_density = 9-3 9-3<br>wall_ewald_zfac = 3<br>pbc = xy <br>fourierspacing = 0.18 <br>
<br><br>Regards<br>Vinoth<br>
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