Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-18 Thread Justin A. Lemkul
Amit Choubey wrote: It seems that i cannot figure out a way to change the absolute reference point (Its the origin by default). Nope. You need to set an actual group of atoms as pull_group0 for a real reference, otherwise the reference point is always the origin. -Justin Amit On Mon,

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey
It seems that i cannot figure out a way to change the absolute reference point (Its the origin by default). Amit On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Yes Justin i understand that. Heres what i think is going on >> >> I dont have any reference g

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Justin A. Lemkul
Amit Choubey wrote: Yes Justin i understand that. Heres what i think is going on I dont have any reference group. Now the COM distance is calculated wrt the origin and whenever the COM is more than half of the box its causing problem. Correct. I think changing the absolute reference to

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey
Yes Justin i understand that. Heres what i think is going on I dont have any reference group. Now the COM distance is calculated wrt the origin and whenever the COM is more than half of the box its causing problem. I think changing the absolute reference to the initial COM of the pull group (usin

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Justin A. Lemkul
Amit Choubey wrote: Hi, I am still not able to see the reason for the periodic distances coming into picture. I guess I don't fully understand your procedure. If you only want to pull to a COM separation of 15 nm, there should be no problem, but yet you're achieving a COM separation of

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey
Hi, I am still not able to see the reason for the periodic distances coming into picture. Also, why pull_geometry = direction_periodic cannot be used with P-coupling; although it seems to do what i want. Amit On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey wrote: > Hi, > > Initially, the pull g

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey
Hi, Initially, the pull group center of mass is at 8.16 nm and i want to pull 15 nm. I started with a box size of 37 nm in the pull direction. The problem occurs when the COM is at 18.5 nm (ie at half the box length). Thanks for the attention. Amit On Mon, Jan 17, 2011 at 11:40 AM, Justin A. L

Re: [gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Justin A. Lemkul
Amit Choubey wrote: Hi all, I am trying to do pulling simulation. Following are the pull parameters pull = umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_group1 = RNA pull_rate1 = 0.01 pull_k1 = 1000 pull_start = yes Everything works fine until the pull group COM reaches half the

[gmx-users] spurious forces while doing pulling simulation

2011-01-17 Thread Amit Choubey
Hi all, I am trying to do pulling simulation. Following are the pull parameters pull = umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_group1 = RNA pull_rate1 = 0.01 pull_k1 = 1000 pull_start = yes Everything works fine until the pull group COM reaches half the box length. The COM posi