hmmm so I use this script
trajin equil_pressure_temp.mdcrd
trajout equil_pressure_temp_reimaged.mdcrd
image origin center familiar
go
but this gives me a segmentation fault
ACTIONS
1> IMAGE familiar by molecule to origin using the center of mass, atom
selection * (All atoms are selected)
IMAGE familiar, center is at origin
Processing AMBER trajectory file equil_pressure_temp.mdcrd
Set 1 ..........Segmentation fault
the system has 150K atoms so could it be a memory issue?
On Wed, Aug 11, 2010 at 2:34 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> yes that was the error a straight line - it did not make any sense. sure it
> is constant and I have check the files and I am doing the reimaging but I
> though the amber coordinates with PBC in VMD would actually do this for one
> but no yet
>
>
> On Wed, Aug 11, 2010 at 2:30 PM, Andrew Purkiss-Trew <
> a.purkiss.mail.cryst.bbk.ac.uk> wrote:
>
>> On Wed, 2010-08-11 at 07:41 -0400, case wrote:
>> > On Wed, Aug 11, 2010, Jorgen Simonsen wrote:
>> > >
>> > > I am equilibrating my system raising the temperature from 0 to 300K -
>> I want
>> > > to start by also equilibrating the pressure doing my simulation in NVT
>> > > enzemble so I set my variables using constraits on my protein backbone
>> (10
>> > > kcal/mol)
>> > >
>> > > ntb = 1,
>> > > cut = 12.0,
>> > >
>> > > when I look at my results in VMD the only thing that has really
>> changed is
>> > > the box which is no longer square but a strange form.
>> >
>> > This sounds like an imaging issue--be sure to re-image using ptraj
>> before
>> > looking at the atomic coordinates in VMD.
>> >
>> > > Furthermore if I plot
>> > > volume and pressure from the output file the volume is increasing and
>> the
>> > > pressure is at 0
>> >
>> > This sounds like a serious problem, since the volume should be constant.
>> > The pressure is reported as zero since it is not computed in NVT
>> > calculations--the zero is just a placeholder. Please double-check that
>> you
>> > are really seeing the volume increase--manually inspect the mdout file,
>> and
>> > look at the last line of the restart file, where the box size is placed.
>> >
>>
>> I believe that this increasing volume is due to the data being
>> misplotted. As you say the pressure is set to zero in the .out file, but
>> the volume isn't even printed. This means that the processing script
>> (process_mdout.perl), which converts the mdout file into the summary
>> files, just gives the time values in the summary.VOLUME file with the
>> corresponding volume data left blank.
>>
>> Some plotting programs this as a straight line (time v time). You need
>> to look at the dimensions in the restart file, to check the volume
>> correctly.
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 11 2010 - 06:00:05 PDT
