[gmx-users] Re: FEP softcore problematics

> Sorry about all of the confusion. Basically, the answer to this > depends on what exactly you're doing. (I should really write all of > this up in a tutorial soon). The way I think about it is that there > are two fundamental principles you need to keep in mind, and you can > do it any way you ca

[gmx-users] Re: FEP softcore problematics

After previous discussions that suggested separating vdw and charge mutations, I thought it was literally a 2 stage process. In one stage I modify all charges (including those for disappearing atoms going to zero) from their starting values to their final values, using 10 lambda points and no so

[gmx-users] Hyperthreading throughput increase

>From my browsing of list archives I can only recall seeing advice that >hyperthreading cannot offer more Gromacs performance. For all I know this remains true if you're trying to use MPI to accelerate single calculations on hyperthreaded processors. However, I have discovered that it may be pos

[gmx-users] Re: free energy tutorial

Hi Bharat, This is the same tutorial that led me astray when I first began trying free energy calculations in Gromacs. I am not sure how close to the experimental value the author intended to get with this hydration free energy tutorial. If you are using a recent version of Gromacs, be aware th

[gmx-users] Re: TI, sampling, sc_power, and sc_alpha

David, I forgot to ask: You said that " the soft core settings that work well for the vdW portion make the charging portion a more "difficult" transformation than normal, and the settings that work well for charging make the vdW portion "difficult". " What settings would you initially suggest t

[gmx-users] Re: TI, sampling, sc_power, and sc_alpha

David and Berk, I enormously appreciate your help in diagnosing my free energy problems. Berk, when you said "I had implemented the alpha=1 option in 3.3 and set it as default" I presume you mean the sc_power=1 option, yes? David, when you talk of splitting the vdW and charge mutations into sep

[gmx-users] TI, sampling, sc_power, and sc_alpha

Greetings once again fellow Gromacs-users, I have seen a substantial and disturbing change in calculated free energy differences between systems run with Gromacs 3.3 and Gromacs 3.3.1. I am trying to determine if these differences are due to the new software, new parameters, insufficient sampli

[gmx-users] PBC and large hydrogen-bonded molecules

Hello fellow Gromacs-users, Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory. When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped some nanometers away from its partner during certain frames. I remembered that there was a note

[gmx-users] Gromacs 3.3.1 MPI/Itanium 2 fails to build

Yes, I did make distclean before configuring with MPI enabled. Matt Ernst Washington State University > [EMAIL PROTECTED] a écrit : >> Hello, >> >> I have successfully built Gromacs 3.3.1 under Linux/Itanium 2 with the >> following >> configure options: >> >> ./configure -with-fft=fftw3 --withou

[gmx-users] Gromacs 3.3.1 MPI/Itanium 2 fails to build

file or directory make[5]: *** [libnb_kernel_ia64_single.la] Error 1 make[5]: Leaving directory `/home/mernst/gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel_ia64_single' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/mernst/gromacs-3.3.1/src/gmxlib/nonbonded' make[3]