[gmx-users] Regarding gromos method in g_cluster

2013-07-30 Thread bipin singh
Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first

Re: [gmx-users] Re: Replica exchange log file inconsistent with mdrun -replex

2013-07-30 Thread Mark Abraham
This should not be silent. Is there nothing in the log file that notes this is occurring? Mark On Tue, Jul 30, 2013 at 11:04 PM, Dejun Lin wrote: > OK. I found the problem is that when -replex is not a multiple of > nstcalcenergy, it'll be converted to nstcalcenergy implicitly. > > > > -- > View

[gmx-users] Re: Replica exchange log file inconsistent with mdrun -replex

2013-07-30 Thread Dejun Lin
OK. I found the problem is that when -replex is not a multiple of nstcalcenergy, it'll be converted to nstcalcenergy implicitly. -- View this message in context: http://gromacs.5086.x6.nabble.com/Replica-exchange-log-file-inconsistent-with-mdrun-replex-tp5010206p5010210.html Sent from the GROMA

Re: [gmx-users] Re: energy conservation / frozen atoms

2013-07-30 Thread Justin Lemkul
On 7/30/13 3:02 PM, S. Alireza Bagherzadeh wrote: On Tue, Jul 30, 2013 at 7:04 AM, wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via

Re: [gmx-users] how to make a rigid entity

2013-07-30 Thread Justin Lemkul
On 7/30/13 1:05 PM, niaz poorgholami wrote: I would like to calculate the PMF between two nanotubes covered with surfactants. for doing this, one nanotube have to hold fixedly and another one have to move as rigid entity. for fixed nanotube I used position restraints, however, I do not know how

Re: [gmx-users] Replica exchange log file inconsistent with mdrun -replex

2013-07-30 Thread Mark Abraham
-replex 100 should emit to the log file every 100 steps. What was your nstlog? Are you sure you are checking the right files? Can you reproduce it? Mark On Tue, Jul 30, 2013 at 8:36 PM, Dejun Lin wrote: > Hi all, > > I'm running a replica exchange simulation using gromacs 4.6.3 with the > comman

[gmx-users] Re: energy conservation / frozen atoms

2013-07-30 Thread S. Alireza Bagherzadeh
On Tue, Jul 30, 2013 at 7:04 AM, wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'he

[gmx-users] Replica exchange log file inconsistent with mdrun -replex

2013-07-30 Thread Dejun Lin
Hi all, I'm running a replica exchange simulation using gromacs 4.6.3 with the command line: mdrun_mpi -deffnm remd_ -multi 64 -replex 100 -nex 262144 I was expecting to get a log entry about the exchange every 100 steps but I only got one every 1000 steps. I wonder if the output was suppressed

[gmx-users] how to make a rigid entity

2013-07-30 Thread niaz poorgholami
I would like to calculate the PMF between two nanotubes covered with surfactants. for doing this, one nanotube have to hold fixedly and another one have to move as rigid entity. for fixed nanotube I used position restraints, however, I do not know how to make a nanotube a rigid entity? I would be p

[gmx-users] AdRess generic kernel for non-bonded interactions

2013-07-30 Thread Sikandar Mashayak
Hi I have a question regarding how non-bonded interactions are determined when running AdRess simulations in Gromacs. In the case in which I have defined all of the system as explicit, i.e., all-atom and NO CG region, are the forces computed in the same manner as if it were doing a normal/all-ato

[gmx-users] Re: trouble with -DGMX_BUILD_OWN_FFTW, crashing in m4? -update/partialy solved

2013-07-30 Thread Jacob Pessin
Thanks for the pointer Mark, I ran a clean make with -j 1 (one thread) and it built just fine. (with gpu=off) Note that a clean make with a single thread and gpu=on still hit the m4 issue not really a bench mark or anything but I ran the em/nvt/npt set from the lysozme tutorial and both the nvt

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
Thank you. So it is only involved in pdb2gmx, but not in the simulation itself - perfect. For some reason I assumed it is checked through the simulation. Writing it now. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192

Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

2013-07-30 Thread Justin Lemkul
On 7/30/13 10:17 AM, Scott Pendley wrote: Justin, Thank you for the continued help. I have copied the text of the mdp file below. It is a little long, so fair warning. The system is a MARTINI Perfect, thanks. coarse grain representation of 1,2-dipalmitoyl-phosphatidyl-glycerole (LHG) su

Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

2013-07-30 Thread Scott Pendley
Justin, Thank you for the continued help. I have copied the text of the mdp file below. It is a little long, so fair warning. The system is a MARTINI coarse grain representation of 1,2-dipalmitoyl-phosphatidyl-glycerole (LHG) surrounded by 700 octanol molecules. Being a neutral MARTINI represe

Re: [gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Justin Lemkul
On 7/30/13 9:58 AM, Valentina wrote: A follow up question - does searching for neighbouring atoms to bond to according to specbond.dat slow down calculation and if so how significantly. I've never seen specbond.dat affect pdb2gmx by more than a few seconds, but it depends on the size of th

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
A follow up question - does searching for neighbouring atoms to bond to according to specbond.dat slow down calculation and if so how significantly. Thanks! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010196.ht

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
Great, thank you, Justin. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010195.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] energy conservation / frozen atoms

2013-07-30 Thread Justin Lemkul
On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote: Hi All, I am simulating a system in which I have two solid surfaces and I keep them frozen during simulations. I also exclude the interactions between its atoms to avoid spurious contribution to the virial pressure due to large forces between

Re: [gmx-users] generating user-defined topologies for surfaces

2013-07-30 Thread Justin Lemkul
On 7/30/13 7:04 AM, Valentina wrote: Hello, I have a strange question with regard to set up of a FF for pdb2gmx for inorganic surfaces (or dendrimers). So previously I used ClayFF (i.e. non-bonded FF) and written input for pdb2gmx - no problem there. Now I want to use the bonded FF. So I have

[gmx-users] generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
Hello, I have a strange question with regard to set up of a FF for pdb2gmx for inorganic surfaces (or dendrimers). So previously I used ClayFF (i.e. non-bonded FF) and written input for pdb2gmx - no problem there. Now I want to use the bonded FF. So I have a unitcell, a residue in what gromacs kn

Aw: [gmx-users] constant force pulling

2013-07-30 Thread lloyd riggs
  Just read your other responses, didnt know it would overide with vector set, but if it doesnt work try the _dim   Stephan Gesendet: Montag, 29. Juli 2013 um 20:42 Uhr Von: kim2811 An: gmx-users@gromacs.org Betreff: [gmx-users] constant force pulling Hi, I am trying to pull/separate a prot

Aw: [gmx-users] constant force pulling

2013-07-30 Thread lloyd riggs
  Your pulling it in all 3 directions at one time.  Also, you should check the COM you want to be pulling from, but I do not know your experimental design.  I would say look at Justins tutorial and example .mdp files.   Stephan Watkins Gesendet: Montag, 29. Juli 2013 um 20:42 Uhr Von: kim2811

[gmx-users] Verlet cut off scheme with tabulated potentials

2013-07-30 Thread Steven Neumann
Dear Gmx Users, I want to run my simulations with tabulated non bonded and bonded parameters on Gromacs 4.6.3. When I ask for 16 cpus it says: that I am not able to use 16 or 8 with cut off scheme Group. So I set up cutoff-scheme = Verlet verlet-buffer-drift = 0.005 ERROR 1 [file grompp.mdp]: