[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Hi, Can anybody tell me why these two tools give different temperature values based on same trajectory and input files? 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg 0.00 508.066786 1.00 496.066137 2.00 501.665712 3.00 498.809896 4.00 499.

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/10/14, 12:49 PM, Rasoul Nasiri wrote: Hi, Can anybody tell me why these two tools give different temperature values based on same trajectory and input files? 1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg 0.00 508.066786 1.00 496.066137 2.00 501.

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Is there any other (not g_energy) tools in GROMACS to estimate T properly? Rasoul On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul wrote: > > > On 7/10/14, 12:49 PM, Rasoul Nasiri wrote: > >> Hi, >> >> Can anybody tell me why these two tools give different temperature values >> based on same tra

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/10/14, 12:58 PM, Rasoul Nasiri wrote: Is there any other (not g_energy) tools in GROMACS to estimate T properly? Why is there a need for that when it's one of the normal functions of g_energy? The values produced from the .edr file are the most accurate that you can get because it st

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? 2- My trajectory is not constrain one as it has been recorded using reactive FF. I need to estimate T with converted trajectory (reaxff>gro). Rasoul On Thu, Jul

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? No, not unless they are assigned as separate tc-grps in the .mdp file, but then (1) you shouldn't be designing something af

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote: > > > On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: > >> Because >> >> 1- Estimation of T for different sub-systems say phases of gas, interface >> and liquid. >> Can be obtained with g_energy? >> >> > No, not unless they are assigned as separate

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/10/14, 9:30 PM, Rasoul Nasiri wrote: On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote: On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy? No, not unless they

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Fri, Jul 11, 2014 at 10:27 PM, Justin Lemkul wrote: > > > On 7/10/14, 9:30 PM, Rasoul Nasiri wrote: > >> On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote: >> >> >>> >>> On 7/10/14, 7:09 PM, Rasoul Nasiri wrote: >>> >>> Because 1- Estimation of T for different sub-systems say p

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Please just tell me how values of obtained T by g_traj can be corrected > when I use trajectory and tpr files of constrain MD simulations (OPLS) as > an input? > T(corrected) = T(g_traj)*natoms/(natoms-nconstraints) Cheers, Tsjerk -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar wrote: > Please just tell me how values of obtained T by g_traj can be corrected > > when I use trajectory and tpr files of constrain MD simulations (OPLS) as > > an input? > > > > > T(corrected) = T(g_traj)*natoms/(natoms-nconstraints) > > T(g_tr

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

Note that two constrained atoms correspond to one constraint. Cheers, T. On Jul 12, 2014 12:01 PM, "Rasoul Nasiri" wrote: > On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar > wrote: > > > Please just tell me how values of obtained T by g_traj can be corrected > > > when I use trajectory and t

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar wrote: > Note that two constrained atoms correspond to one constraint. > > C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore 66300 will be total constrained atoms in ce

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrained atoms due to hydrogens which have been connected to carbon atoms. Number of molecules 2550 therefore

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote: > > > On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: > >> On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar >> wrote: >> >> Note that two constrained atoms correspond to one constraint. >>> >>> >>> >> >> C12H26 >> >> 26 constrained atoms due to

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote: On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar wrote: Note that two constrained atoms correspond to one constraint. C12H26 26 constrain

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote: > > > On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: > >> On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote: >> >> >>> >>> On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: >>> >>> On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar wrote: >

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On 7/13/14, 8:41 PM, Rasoul Nasiri wrote: On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote: On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote: On 7/12/14, 7:25 AM, Rasoul Nasiri wrote: On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wasse

Re: [gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

On Mon, Jul 14, 2014 at 12:51 PM, Justin Lemkul wrote: > > > On 7/13/14, 8:41 PM, Rasoul Nasiri wrote: > >> On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote: >> >> >>> >>> On 7/13/14, 7:11 PM, Rasoul Nasiri wrote: >>> >>> On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote: