Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

David, My conclusion so far is that trr file must be used for rerun (we learn every day, isn't it fabulous !) and I do not see the bug you pointed out but probably due to the system I run !! Well, that sounds like good news. If we accept to not understand why you got a different result,

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Xavier, > My conclusion so far is that trr file must be used for rerun (we learn > every day, isn't it fabulous !) > and I do not see the bug you pointed out but probably due to the system > I run !! Well, that sounds like good news. I am not surprised that the reduced precision trajectories giv

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

David, I'll try to explain a bit better and I attached a gziped pdf file containing a reduced set of energies that I sent at my first post. I, too, am slightly confused about what exactly the differences are you're seeing. Could you perhaps make a little table or something? Partly, I just do

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Xavier, I basically rerun a simulation, both in xtc and trrformat,using slightly different tpr file, varying the gro file used to construct it, and different gmx version, 3.2 and3.3. From those rerun I extracted and compared the bondedand non-bonded energies.The most stricking is that I do not see

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Dear Mark, I basically rerun a simulation, both in xtc and trr format, using slightly different tpr file, varying the gro file used to construct it, and different gmx version, 3.2 and 3.3. From those rerun I extracted and compared the bonded and non-bonded energies. The most stricking is that

Re: [gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Xavier Periole wrote: The energies indicate that: 0) I see a systematic difference with the original energies (not significant), but using the trr file helps getting better. 1) I do not see ANY difference between the rerun using the two tpr file (Unexpected ?!?!) 2) I do not see significant

[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3: the energy file

I forgot the energy file. It is now attached. XAvier -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Tel: +31-503634329 Fax: +31-503634398 email: [EMAIL PROTECTED] web-

[gmx-users] mdrun -rerun with gmx3.2 and gmx3.3

Dears, I have reruning simulations using gmx3.2 and found out some deferences between the original and rerun energies. I found the posts made by David Mobley and Mickael Shirts about this issue. Accordingly I downloaded gmx3.3 and compiled it with the fixed md.c for the rerun, found in the bugzi