VMD-L Mailing List

From: Hitesh Patel (hiteshpatel379_at_gmail.com)
Date: Mon Nov 14 2011 - 11:09:41 CST

thanks fro help..

pbc wrap -compound fragment -center com -centersel "resid 35" -all
worked!!!

Regards,

Hitesh Patel

On Mon, Nov 14, 2011 at 5:17 PM, Hitesh Patel <hiteshpatel379_at_gmail.com>wrote:

> Hello,
> pbc wrap -compound fragment -all
> This command did not generate stretched bonds.. But, protein is going out
> of the box.
>
> I tried to keep the resid 35 at centre.. by
> pbc wrap -compound fragment -centersel "resid 35" -all
> But, It didn't work. It gave the same result as above command.
>
> Thanks,
>
> Regards,
>
> Hitesh Patel
>
>
>
> On Mon, Nov 14, 2011 at 4:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>> On Mon, 2011-11-14 at 15:48 +0100, Hitesh Patel wrote:
>> > Hello,
>> > I have MD simulations trajectories of 3ns from desmond. but, after 2ns
>> > complex is going out of box. How can I wrap in a way, that everytime
>> > molecule stay at the centre of box.
>> > I tried "pbc wrap -all" but,it makes stretched bonds. After that I
>> > tried to unwrap. and again molecule looks out of box.
>> > What commands should I use ?
>>
>> when using pbc wrap, make sure you have the right
>> '-compound' flag. the default is wrapping individual
>> atoms, which will result in those "stretched" bond.
>> to retain intact molecules, you should try to wrap
>> with '-compound fragment' added instead.
>>
>> cheers,
>> axel.
>>
>> > Thanks,
>> > Regards,
>> > Hitesh
>>
>>
>>
>