Re: [gmx-users] using more processors for g_mindist

2012-02-29 Thread Mark Abraham
On 29/02/2012 9:05 PM, aiswarya pawar wrote: Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist What makes you think there is only one atom satisfying that cutoff? 5.00e+02 518 42680 5.01e+02

Re: [gmx-users] using more processors for g_mindist

2012-02-29 Thread aiswarya pawar
Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02

Re: [gmx-users] using more processors for g_mindist

2012-02-29 Thread Mark Abraham
On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein a

Re: [gmx-users] using more processors for g_mindist

2012-02-29 Thread aiswarya pawar
Mark, i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. Thanks On Wed, Feb 29, 2012 at 12

Re: [gmx-users] using more processors for g_mindist

2012-02-28 Thread Mark Abraham
On 29/02/2012 6:01 PM, aiswarya pawar wrote: Mark, Right now am computing distance between each protein atom against all water atoms, That's expensive. mdrun goes to great lengths to speed up computing billions of distances. which is taking too long for 5ns run. i cant reduce the frames

Re: [gmx-users] using more processors for g_mindist

2012-02-28 Thread aiswarya pawar
Mark, Right now am computing distance between each protein atom against all water atoms, which is taking too long for 5ns run. i cant reduce the frames either the number of water atoms. So is there any alternate. Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham wrote: > On 29/02/2012 5:17

Re: [gmx-users] using more processors for g_mindist

2012-02-28 Thread Mark Abraham
On 29/02/2012 5:17 PM, aiswarya pawar wrote: Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? No. If it will take too long, you need to reduce your number of frames (trjcon

[gmx-users] using more processors for g_mindist

2012-02-28 Thread aiswarya pawar
Dear all, Am running g_mindist on large number of atoms, i would like to know whether i can run this on more than one processors say 8 processors to speed up the task? and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- gmx-users mailing listgmx-users@gromacs.org ht