[gmx-users] Regarding protocol of g_lie module

Dear users, I want to calculate linear interaction energy for my protein-ligand complex using g_lie module in Gromacs. I have ran two different simulations of ligand, one with protein and other with water. But I am getting same values for GBind while using g_lie for both simulations. Can anyone h

[gmx-users] g_mmpbsa compilation error

Hi, I am trying to compile g_mmpbsa with APBS for gromacs-5.1.2. APBS and gromacs installed properly but during cmake for g_mmpbsa I am facing the following error: -- Found z library: /usr/lib/x86_64-linux-gnu/libz.so CMake Error at cmake/FindGROMACS.cmake:203 (list): list index: 2 out of range

[gmx-users] g_mmpbsa compilation error

Hi, I tried to compile g_mmpbsa with APBS but no success. Firstly I was facing the error regarging geoflow directory and libraries (while installing APBS), I somehow solved that but now I am facing the following error while cmake (g_mmpbsa): -- Found z library: /usr/lib/x86_64-linux-gnu/libz.so C

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

/CMakeLists.txt:62 (find_package) -- Found Gromacs include directory: /usr/local/gromacs/include -- Configuring incomplete, errors occurred! Please help. Thanks. *Neha* On Wed, Aug 30, 2017 at 10:42 AM, neha chaudhary wrote: > Hi, > > I will download and install APBS and try again. &

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hi, I will download and install APBS and try again. I have already tried pre-compiled version of g_mmpbsa from the link you suggested. Thanks Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pra

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hello, I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I compile it with APBS? Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, On Wed, Aug 30, 2017 at 10:23

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Thank you for replying, I have compiled g_mmpbsa without apna. I have tried with pre-compiled binary as well but no success. On 29-Aug-2017 3:45 PM, "Nikhil Maroli" wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (scinik...@gmail.com)

[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Dear Sir/Ma'am, I am trying to run g_mmpbsa for gromacs-5.1.2. It is working fine for MM energy and apolar energy but when I am trying to run this for polar energy, g_mmpbsa run is stopping giving error: Segmentation fault (core dumped). Previously I was using gromacs 4.6 with same g_mmpbsa versi

Re: [gmx-users] Regarding using random seed

= yes gen-seed = -1 Best Regards, *Neha* Research Scholar, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, On Wed, Mar 9, 2016 at 6:36 PM, Tsjerk Wassenaar wrote: > Right! > > T. > On Mar 9, 2016 12:24 PM, &qu

Re: [gmx-users] Regarding using random seed

ttp://manual.gromacs.org/online/mdp_opt.html#vel) > > Best, > > Tsjerk > > > On Wed, Mar 9, 2016 at 11:16 AM, neha chaudhary < > nehachaudhary...@gmail.com> > wrote: > > > Thanks Tsjerk for replying, > > > > I want to ask one more question that t

Re: [gmx-users] Regarding using random seed

s using elastic-network modeling, > like with the ElNemo server. Mind to first energy minimize the resulting, > extrapolated structures, as they may be stretchedhere and there. > > Hope it helps, > > Tsjerk > > On Wed, Mar 9, 2016 at 10:54 AM, neha chaudhary < > nehachaud

[gmx-users] Regarding using random seed

Hello there, Can anyone tell me how can I start my MD simulations with different starting structure (random seed) for my protein-ligand complex. Can I start with different sets of coordinates and velocities? If yes, how? Thanks, *Neha* Research Scholar, Centre for Computational Biology and Bio

[gmx-users] Regarding groups making by make_ndx

Hello Sir, I want to make a new group that contain 2-3 amino acid residues present in protein. But when I am running nvt simulation with this new group error message like multiple t-coupling groups in (1 and 3). So, I am using "splitres" option in make_ndx module of gromacs to separate number of r