Re: [gmx-users] correlation function

Jamie Seyed wrote: On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul > wrote: Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I

Re: [gmx-users] Re: Re: Pull to separate dimer

Ragnarok sdf wrote: Hi Justin. So for each window, I would turn pull_rate to zero in order to get a system in equilibrium? Yes, I believe that is correct. The umbrella potential is used to restrain the configuration within a given window. And then the lambda value would be equal to

[gmx-users] Re: Re: Pull to separate dimer

Hi Justin. So for each window, I would turn pull_rate to zero in order to get a system in equilibrium? And then the lambda value would be equal to each of the sampling distances? How would I justify using this pull_rate and pull_k1 values in order to obtain my pulling trajectory? i.e. is there so

[gmx-users] Re: gmx-users Digest, Vol 64, Issue 147

Hi Justin. So for each window, I would turn pull_rate to zero in order to get a system in equilibrium? And then the lambda value would be equal to each of the sampling distances? How would I justify using this pull_rate and pull_k1 values in order to obtain my pulling trajectory? i.e. is there so

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should get

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should

Re: [gmx-users] correlation function

Hi Justin and Mark, Thanks. Actually I made a mistake and it seems going to the zero (even negative!) --But I wanted to know how I can write my command to get only one graph (average of all instead of all of them). I read the manual chapter-8 and by average I mean I should get one curve starting at

Re: [gmx-users] correlation function

Justin A. Lemkul wrote: Jamie Seyed wrote: Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Huh? The average has nothing to do with calculating the autocorrelation func

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starti

Re: [gmx-users] Re: Pull to separate dimer

Ragnarok sdf wrote: Hi Justin, yes the intention is to pull the dimer apart within the plane of the bilayer. I've ran a few more tests changing a few of the parameters and got to one set that pulls my dimer apart apparently in a "friendly" way, I mean, using g_dist to monitor th

[gmx-users] Re: Pull to separate dimer

> > Hi Justin, yes the intention is to pull the dimer apart within the plane of > the bilayer. I've ran a few more tests changing a few of the parameters and > got to one set that pulls my dimer apart apparently in a "friendly" way, I > mean, using g_dist to monitor the COM distances I got an incre

Re: [gmx-users] correlation function

Hi Justin, Thanks again. I made and used coord.xvg with command g_analyze -f coord.xvg -ac autocorr.xvg and I got a huge file that I think I need to average over it. Would you please let me know how I can get a nice average curve? Also I can see that all of them starting at 1, but I do not thi

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Justin, Thanks for the answer. I want to calculate auto-correlation function of R(x,y,z). I mean , .../Many Thanks in Advance/Jamie Coordinates? Use g_traj. -Justin On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul > wrote: Jamie Se

Re: [gmx-users] correlation function

Hi Justin, Thanks for the answer. I want to calculate auto-correlation function of R(x,y,z). I mean , .../Many Thanks in Advance/Jamie On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > >> Hi Mark, >> Thanks for the answers. I want to use g_analyze but it needs

Re: [gmx-users] correlation function

Jamie Seyed wrote: Hi Mark, Thanks for the answers. I want to use g_analyze but it needs a file graph.xvg as an input file. How can I get that for calculation of auto-correlation function? Many Thanks in Advance/Jamie The graph.xvg file contains the data for which you want to obtain the

Re: [gmx-users] correlation function

Hi Mark, Thanks for the answers. I want to use g_analyze but it needs a file graph.xvg as an input file. How can I get that for calculation of auto-correlation function? Many Thanks in Advance/Jamie On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham wrote: > Jamie Seyed wrote: > >> Hi Mark, >> Thanks

[gmx-users] Re: pdb2gmx problem

leila karami wrote: Hi I have PDB file of DNA (PDB ID: 1D49). I intend generate topology file by pdb2gmx. One error is created: (atom O5 in residue DCYT 1 not found in rtp entry with 21 atom while sorting atom). 2 notes: 1: I checked rtp file for used force field. In rtp file, there is [DC

Re: [gmx-users] DNA problem

mojdeh akhavan wrote: Hi I have PDB file of DNA (PDB ID: 1D49). I intend generate topology file by pdb2gmx. One error is created: (atom O5 in residue DCYT 1 not found in rtp entry with 21 atom while sorting atom). 2 notes: 1: I checked rtp file for used force field. In rtp file, there is [DCYT]

[gmx-users] DNA problem

Hi I have PDB file of DNA (PDB ID: 1D49). I intend generate topology file by pdb2gmx. One error is created: (atom O5 in residue DCYT 1 not found in rtp entry with 21 atom while sorting atom). 2 notes: 1: I checked rtp file for used force field. In rtp file, there is [DCYT] , [DTYM] , [DADE] and [D

[gmx-users] Visit my Netlog profile

Hey, I have created a Netlog profile with my pictures, videos, blogs and events and I want to add you as a friend so you can see it. You first need to register on Netlog! When you log in, you can create your own profile. Take a look: http://en.netlog.com/go/mailurl/type=invite_1&mailid=42803035

[gmx-users] [Fwd: Please solve my problem]

To, David van der Spoel Dear Sir, I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a problem. I am giving job for 50 steps step size 0.002ps (total 1ns) but my job is stopped after 47 steps. when i run this on 4 processors. But the same job is completed on 2