[gmx-users] RMS deviation after position restraint dynamics

Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little)

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Chih-Ying Lin wrote: HI How can i know if the protein swell during the MD simulation? What are those indications to "see" the swollen protein? How do you define the term "swelling?" This again sounds like another issue on defining your own criteria for the expected behavior and reading th

[gmx-users] How can i know if the protein swell during the MD simulation?

HI How can i know if the protein swell during the MD simulation? What are those indications to "see" the swollen protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

Re: [gmx-users] Segmentation fault

Chih-Ying Lin wrote: Hi I run the simulation on MPI. first, i make constraints=all bond => successful second, i make constraints=none => segmentation fault is the "segmentation fault" coming from the NONE bond-contraints? The rest of your parameters and whatever is in your system is no

[gmx-users] Segmentation fault

Hi I run the simulation on MPI. first, i make constraints=all bond => successful second, i make constraints=none => segmentation fault is the "segmentation fault" coming from the NONE bond-contraints? Thanks Lin ___ gmx-users mailing listgmx-u

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

On Sun, 2009-05-17 at 10:56 -0700, Semen Esilevsky wrote: > Ok, I have found the bug. > In file xdrfile_xtc.h conditional directives should be "#ifdef __cplusplus", > not "#ifdef CPLUSPLUS" ! > After that I have functional text program. > Now, I tried to make a test with C++ with this simplest

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

Ok, I have found the bug. In file xdrfile_xtc.h conditional directives should be "#ifdef __cplusplus", not "#ifdef CPLUSPLUS" ! - Original Message From: Semen Esilevsky To: Discussion list for GROMACS users Sent: Sunday, May 17, 2009 8:47:44 PM Subject: Re: [gmx-users] How to compi

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

Well, it seems that changing all bools to ints doesn't help. It still work with C but not with C++. I changed bools to ints and recompiled the library. Then I copied xdrfile_c_test.c, headers and the recompiled library to the separate directory. gcc -c xdrfile_c_test.c gcc xdrfile_c_test.o

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

Semen Esilevsky wrote: Ok, I've submitted a bug report. Concerning changing bools to ints. Where should I do this? In the libdrfile source code. - Original Message From: David van der Spoel To: Discussion list for GROMACS users Sent: Sunday, May 17, 2009 2:57:36 PM Subject: Re: [

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

Ok, I've submitted a bug report. Concerning changing bools to ints. Where should I do this? - Original Message From: David van der Spoel To: Discussion list for GROMACS users Sent: Sunday, May 17, 2009 2:57:36 PM Subject: Re: [gmx-users] How to compile C++ propgram with xdrfile libr

Re: [gmx-users] How to compile C++ propgram with xdrfile library?

Semen Esilevsky wrote: Dear All, I'm trying to add the functionality of reading xtc to my own C++ code for a long time, so I was looking forward for libxdrfile release. Finally it is released and I tried it. I included xdrfile_xtc.h and immediately got the following error: /usr/local/gentop/i

[gmx-users] How to compile C++ propgram with xdrfile library?

Dear All, I'm trying to add the functionality of reading xtc to my own C++ code for a long time, so I was looking forward for libxdrfile release. Finally it is released and I tried it. I included xdrfile_xtc.h and immediately got the following error: /usr/local/gentop/include/xdrfile/xdrfile.h

Re: [gmx-users] Molecule Jumps

darre...@ece.ubc.ca wrote: Hi All, I have an array of molecules above a grapehene sheet in my simulation. However, when I look at my trajectory file (.trr) in VMD the array of molecules is split into 4 sections with each section located at what looks to be the corners of the simulation box. And t

[gmx-users] Molecule Jumps

Hi All, I have an array of molecules above a grapehene sheet in my simulation. However, when I look at my trajectory file (.trr) in VMD the array of molecules is split into 4 sections with each section located at what looks to be the corners of the simulation box. And the graphene sheet does not s