[gmx-users] Installing DSSP

Hello all, I am trying to install dssp in centos 7 for determining the secondary structure of a protein in combination with do_dssp. These are the steps I followed: 1. installation directory : /opt/apps/dssp/dssp-2.2.1/ 2. but there is no dssp executable in the dssp-2.2.1 directory 3. however t

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

Thank you, Mark. I am now trying to install devtoolset-2. Regarding Cygwin version, I must clarify that, although the compilation is successful, I got an error message when performing "make check": 95% tests passed, 1 tests failed out of 20 The following tests FAILED: 12 - SimdUnitTests (SEGFAUL

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

Hi, These are linking errors that look like they are from not linking the appropriate version of the C++ standard library. I highly recommend leaving the system libraries alone on redhat systems, and instead compiling with the devtoolset packages. Thanks for the Cygwin report. People often report

[gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

Hi Colleagues, I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5 server; I have updated GCC compiler and all dependent libraries (tried GCC 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7, which is too old.) I used the commmand export CC=gcc exp

Re: [gmx-users] Reflecting Boundary Condition

Dear Prof. van der Spoel, Thanks a lot for your reply. As far as I understand, the wall potential implemented in gromacs, can only handle reflective boundary condition along one of the three dimensions. What I exactly want is to put reflecting boundary conditions on all the 3 directions. Let's a

Re: [gmx-users] Clarification please

Hi, We switched version numbering scheme to reflect that we make one release per year with new content. 5.1.x was the 2015 release - all those have the same nominal content but with e.g. more bugs fixed. Likewise 2016.x, which will have new things in it compared with 5.1.x (see the release notes o

Re: [gmx-users] Linker error during GMX make

Dear Szilárd, I finally downloaded the package again and repeated cmake/make. For whatever reason, it finally linked flawlessly. Thanks for your help! Best, Clemens Zitat von Szilárd Páll : On Mon, Jan 30, 2017 at 1:25 PM, Clemens Grimm wrote: Dear All, I am doing a cmake . -DGMX_GPU=

[gmx-users] Clarification please

Can someone explain the existence and difference of versions 5.1.4 and 2016.1. These seem to occur in parallel and lead me to confusion on which to compile and use. Paul Schlesinger -- Paul H. Schlesinger MD, PhD Washington University School of Medicine -- Gromacs Users mailing list * Please

[gmx-users] Post-analysis of residue residue interactions

Dear gromacs users We've run umbrella sampling simulations (with pull) of proteinA/ProteinB dimer turning into two separate monomers We have 25 simulation windows each of 10 ns MD (1000 frames) and proteins containing 132 residues We now want to calculate interaction energy (VDW Elec) between e

[gmx-users] Positions for Ph.D. candidates in biomolecular modeling

Dear colleagues, we are seeking two Ph.D. candidates for newly opened positions in our laboratory - for details see http://labbit.eu/2017/01/12/two-positions-for-ph-d-candidates-available/ Please forward to prospective students. Thank you. Best regards, Jan -- _

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

Indeed same Thomas has good points I could have mentioned. Reduce the interface gap to a minimum of the system ca get stuck in stupid state … the two side should see each other, once they start merging it is fast. XAvier. > On 01 Feb 2017, at 20:01, Thomas Piggot wrote: > > I've actually u