Re: [gmx-users] number of DD cells

2011-03-04 Thread Mark Abraham
On 05/03/11, "Justin A. Lemkul" wrote: > > > Moeed wrote: > >Hello, > > > >I am attempting to increase the density using NPT. As I increase the > >pressure to compress the system after some steps simulation crashes. I > >thought maybe its becasue I am compressing too fast but even when I ta

Re: [gmx-users] number of DD cells

2011-03-04 Thread Justin A. Lemkul
Justin A. Lemkul wrote: Moeed wrote: Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33,

Re: [gmx-users] number of DD cells

2011-03-04 Thread Justin A. Lemkul
Moeed wrote: Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance,

Re: [gmx-users] number of DD cells

2011-03-04 Thread Moeed
Hello Justin, Thanks. 1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-

Re: [gmx-users] number of DD cells

2011-03-04 Thread Justin A. Lemkul
Moeed wrote: Hello, I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error c

[gmx-users] number of DD cells

2011-03-04 Thread Moeed
Hello, I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density

Re: [gmx-users] number of DD cells

2010-12-26 Thread Justin A. Lemkul
Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running

RE: [gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan
-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: > Hi, > > I am

Re: [gmx-users] number of DD cells

2010-12-26 Thread Mark Abraham
On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but

[gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan
Hi, To my earlier post on number of DD cells.i included -dds 0.6 and everything seems to run fine. Is this the possible solution to the error or is there other way to handle this warning ? Kind regards, chetan. ---

[gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan
Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning " The X-size of