[gmx-users] Thank you

Respectable Mark Thank you very much for your immediate response. I have added new atom type in the ffgmx.atp file and also modified ffgmx.itp, ffgmxnb.itp. After that the pdb2gmx worked. I used genbox to add water in the oxygen molecule system. For now I have taken only 2 oxygen molecules with

Re: [gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

* Chris Neale [2009-01-17 10:11:34 -0500]: Hello, For my systems, I have been unable to get g_mindist -pi to function unless I roll back to gmx 3.3.1. Would somebody please test their 4.0.2 (and perhaps 3.3.3) installations to see if the error is repeatable or perhaps is somehow related to

RE: [gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

Hi, I never noticed this because I always used -s. Supply a tpr file with -s in addition to -n and it will work. I fixed this for 4.0.3 such that with -pi it automatically uses -s as well. Berk > Date: Sat, 17 Jan 2009 10:11:34 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org >

[gmx-users] g_mindist -pi gives segfault in 3.3.3 and 4.0.2 but not 3.3.1

Hello, For my systems, I have been unable to get g_mindist -pi to function unless I roll back to gmx 3.3.1. Would somebody please test their 4.0.2 (and perhaps 3.3.3) installations to see if the error is repeatable or perhaps is somehow related to my installation? Related output from 3.3.3 w

Re[2]: [gmx-users] units...

Justin, Thank you! It's pretty clear now. Vitaly JAL> Vitaly Chaban wrote: >> Justin, >> >> So the values in the respective columns are pure and ^2 of >> the particles of the same kind (no additional operations made)? >> JAL> Correct, there is nothing mathematical about the xmgrace syntax.

Re: [gmx-users] units...

Vitaly Chaban wrote: Justin, So the values in the respective columns are pure and ^2 of the particles of the same kind (no additional operations made)? Correct, there is nothing mathematical about the xmgrace syntax. -Justin Vitaly JAL> Vitaly Chaban wrote: Hello, Sorry for an eviden

Re[2]: [gmx-users] units...

Justin, So the values in the respective columns are pure and ^2 of the particles of the same kind (no additional operations made)? Vitaly JAL> Vitaly Chaban wrote: >> Hello, >> >> Sorry for an evidently stupid question. I use g_dipoles to calculate >> the total dipole moment of the cell evolut

Re: [gmx-users] units...

Vitaly Chaban wrote: Hello, Sorry for an evidently stupid question. I use g_dipoles to calculate the total dipole moment of the cell evolution. In aver.xvg the following line is present: @ s0 legend "< |M|\S2\N >" @ s1 legend "< |M| >\S2\N" |M| is a modulus of dipole vector. But what are "\S2

Re: [gmx-users] units...

* Vitaly Chaban [2009-01-17 16:18:29 +0200]: Hello, Sorry for an evidently stupid question. I use g_dipoles to calculate the total dipole moment of the cell evolution. In aver.xvg the following line is present: @ s0 legend "< |M|\S2\N >" @ s1 legend "< |M| >\S2\N" |M| is a modulus of dipole v

[gmx-users] units...

Hello, Sorry for an evidently stupid question. I use g_dipoles to calculate the total dipole moment of the cell evolution. In aver.xvg the following line is present: @ s0 legend "< |M|\S2\N >" @ s1 legend "< |M| >\S2\N" |M| is a modulus of dipole vector. But what are "\S2\N"? Is N a number of par

Re: [gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

thank you for the rational explanation. but is the free energy change in the charge on/off step(~10kJ/mol) small enough to ignore the flucturations? The free energy change in the LJ mutation step is about 8kJ/mol. On Fri, Jan 16, 2009 at 11:56 PM, Jochen Hub wrote: > friendli wrote: > > Dear al