[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: Regarding particles moving outside the box

From: Martin Kaiser
Subject: Re: Regarding particles moving outside the box
Date: Thu, 13 Jan 2022 13:51:46 +0100

Hey Chandra,

I assume that you use vmd for visualization. Try using the command "pbc wrap" (without the quotation marks) in the vmd console. Espresso stores the un-wrapped coordinates in the vtf file and this command tells vmd to fold them into the box.
Of course, check that pbc are activated in you system

Alternatively, you can change the behaviour of writevcf() in the file 


to print part.pos_folded instead of part.pos. This makes espresso print the folded coordinates directly into the vtf file.


On Jan 13, 2022 13:12, chandra shekhar maurya <> wrote:

Hello everyone,
I am simulating tutorial "Ferrofluid - Part 3". Which is a 3D system. I am using a vtf file to visulise the particles within the box. But the particles move outside the box. Is it the problem of the system or vtf file?
How can I fix it?

equil_rounds = 1000
equil_steps = 10
equil_cycle =1
from import vtf
fp = open('trajectory_monomer2.vtf', mode='w+t')
vtf.writevsf(system, fp)
vtf.writevcf(system, fp)
for i in range(equil_rounds):
for j in range(equil_cycle):
vtf.writevcf(system, fp)

Thanks & Regards
Chandra Shekhar Maurya
Mechanical Eng. Dept.
Indian Institute of Technology Patna
Contact No:9793572837

reply via email to

[Prev in Thread] Current Thread [Next in Thread]