[gmx-users] Free energy calculation of a charged system

Hello, I need an advise on how it is better to approach the ThermoD integration of such system: +vely charged inorganic layer, filled with water and counterbalanced by -ve organics Do I integrate out organics both VdW and Coulomb, making the system have total +ve charge at lambda = 1 OR: Do I i

Re: [gmx-users] Free energy calculation of a charged system

Hi! Thank you for reply. You have lost me there, tbh. I think I didn't make it clear, I have either organic -vely changed molecule or Cl-. Those counterbalance the +vely charged material. Therefore, I either have organics or clorine. So, if I do TI and completely decouple vow and charges: couple

[gmx-users] free energy of removal of a molecule from the bulk

I am running thermodynamic integration and I wanted to remove 1 molecule of water from bulk (as a test). But I am not sure how to specify it in the map file with couple-moltype: If I specify SOL I will be decoupling all of it, if I rename that specific molecule to something else, I get: The [mo

Re: [gmx-users] free energy of removal of a molecule from the bulk

Thank you Justin. This is what I have tried, but obviously gone wrong with [settles]. I'll try again. V -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-of-removal-of-a-molecule-from-the-bulk-tp5015333p5015344.html Sent from the GROMACS Users Forum mailing list ar

[gmx-users] genconf of box of a few types of molecules

Hello, It would be good to know, if I am missing something out here. Thank you! I have a set up box of a few components: a material layer (MIN), peptide (ASP) and water (SOL). system.gro file it looks like this: 1MIN ... 2MIN ... 3ASP ... 4ASP ... 5SOL ... 6SOL ... system.top ... [ molecules ]

Re: [gmx-users] Potential for Frozen atoms

I am not sure I understand your approach - "box containing ... very far away to make the system charge zero." Is your far further than cut off? V -- View this message in context: http://gromacs.5086.x6.nabble.com/Potential-for-Frozen-atoms-tp5015870p5015878.html Sent from the GROMACS Users Foru

Re: [gmx-users] how to use g_angle to get the average dihedral angle ?

Hi, You need to make index containing all the angles you want to calculate the angle for. You could just manually edit the .ndx by combining all entries under one header, i.e. deleting all headers but first. Hope it helps, V -- View this message in context: http://gromacs.5086.x6.nabble.com/how

Re: [gmx-users] genconf of box of a few types of molecules

Thank you, this makes perfect sense! -- View this message in context: http://gromacs.5086.x6.nabble.com/genconf-of-box-of-a-few-types-of-molecules-tp5015876p5015897.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archi

Re: [gmx-users] Potential for Frozen atoms

Hi, As Vitaly said, you are mixing the methods. If you want to find out the potential between 2 atoms, why don't you just go into the FF, pick out relevant parameters from there and plot it. So for 2 non-bonded atoms the contribution would be VdW and Coulomb. Putting things further than cut-off

[gmx-users] step 0Segmentation fault: 11

bonded & angle potentials. I would be very happy to hear any advises, Thank you V Full md.log: valentina$ more md.log Log file opened on Tue Nov 26 22:07:50 2013 Host: oparin01.earthsci.dur.ac.uk pid: 18263 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6 Precision:

Re: [gmx-users] step 0Segmentation fault: 11

The problems I have eliminated: 1. Number of processors and threads - I am running on 1 2. Atomic overlap - none I have checked my bonded wells and my atomic distances are very similar. The init was originally minimised with DFT. 3. LINCS - I get same error if I run with or without constraints 4

Re: [gmx-users] step 0Segmentation fault: 11

Thank you for your reply. I am now suspecting charges to be a problem. -- View this message in context: http://gromacs.5086.x6.nabble.com/step-0Segmentation-fault-11-tp5012832p5012857.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Ple

Re: [gmx-users] step 0Segmentation fault: 11

I still cannot resolve this problem. Is there any way to find out what is causing Segmentation Fault? Normally Gromacs provides quite comprehendible errors, but this one. I have checked the charges against DFT. I also have the output of the system simulated with Discover. I am using that force f

[gmx-users] Install errors

no input files CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 (message): Error generating /Users/Valentina/Software/gromacs-4.6.6/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_

Re: [gmx-users] Install errors

Thanks! 2014-08-20 14:05 GMT+02:00 Mark Abraham : > Hi, > > You should be using a supported host compiler for your version of CUDA > (check its docs, probably gcc 4.7 or 4.8, for example), rather than clang. > > Mark > > > On Wed, Aug 20, 2014 at 9:59 AM, Valentina