Re: [gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

Hi all, I have encountered the same problem. With this command: ./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi "make mdrun" works well When i used the same option with gmx 4.5.4 ./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi "make mdrun" did not work. The com

Re: [gmx-users] Is there still interest in rigid-body simulation?

Hi Adam, because some time ago I was involved in a rigid-body MD project, I am interested to known if you are following a published or known method. I do not know your rigid-body algorithm, however I would suggest you to take care on rotations, because they are not a simple task. Good luck L

Re: [gmx-users] FEP and loss of performance

> there's no record of it in redmine, it likely won't get addressed. > Gromacs is undergoing major changes at the moment, so the core developers > are quite busy with other priorities. > > -Justin > > Luca Bellucci wrote: > > I posted my t

Re: [gmx-users] FEP and loss of performance

3209687.978 > 100.0 > -- > --- > > > You may want to provide an mdp file and topology, etc. so someone can > > see if they can reproduce your problem. > > I agree that would

Re: [gmx-users] FEP and loss of performance

> > >/ I expected a loss of performance, but not so drastic. > > > > />/ Luca > > />/ > > />>/ Load balancing problems I can understand, but why would it take > > longer />>/ in absolute time? I would have thought that some nodes would >

Re: [gmx-users] FEP and loss of performance

sitting idle, but this should not cause an increase in the > overall />>/ simulation time (15x at that!). > />>/ > />>/ There must be some extra communication? > />>/ > />>/ I agree with Justin that this seems like a strange thing to do, but > />

Re: [gmx-users] FEP and loss of performance

n that this seems like a strange thing to do, but > still I think that there must be some underlying coding issue (probably > one that only exists because of a reasonable assumption that nobody > would annihilate the largest part of their system). > > Chris. > > Luca Bellucci

Re: [gmx-users] FEP and loss of performance

Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not "Protein_chaim_P". Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. However the problem exist and the performance loss is v

[gmx-users] FEP and loss of performance

Dear all, when I run a single free energy simulation i noticed that there is a loss of performace with respect to the normal MD free_energy= yes init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = Protein_Chain_P couple-lambda0 = vdw-q couple-lambda0 = none couple-intramol= yes

[gmx-users] Setting the C6 LJ term for OPLSA FF

Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it works i

[gmx-users] Setting the C6 LJ term for OPLSA FF

Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it work in

[gmx-users] couple-moltype for two molecules

Dear all, I tried to use "couple-moltype=Protein Ligand" directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used "couple-moltype=Protein" to ann

[gmx-users] couple-moltype for two molecules

Dear all, I tryed to use "couple-moltype=Protein Ligand" directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used "couple-moltype=Protein" to ann

[gmx-users] couple-moltype for two molecules

Dear all, I tryed to use "couple-moltype=Protein Ligand" directive to annihilate both protein and ligand molecules using free energy method. I realized that couple-moltype key works for only one molecule type. Is it right? To perform the same annihilation I used "couple-moltype=Protein" to ann

Re: [gmx-users] scaling of replica exchange

Hi Valeria, > Dear all, > I am making some tests to start using replica exchange molecular dynamics > on my system in water. The setup is ok (i.e. one replica alone runs > correctly), but I am not able to parallelize the REMD. Details follow: > > - the test is on 8 temperatures, so 8 replicas > -