Thank you! I have missed it somehow. I can still use my xtc trajectory. Steven
On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo <j...@um.es> wrote: > The trr file has something wrong. Look at "Coords", it has 0 frames > > You may have forgotten to set nstxout to a non-zero value? > > Javier > > El 09/05/12 16:10, Steven Neumann escribió: > > I added one water molecule in my topology to all water molecules: > > [ molecules ] > ; Compound #mols > Alanine 40 > SOL 724 > > Maybe I should add aditional line like: > > [ molecules ] > ; Compound #mols > Alanine 40 > SOL 723 > SOL 1 > > What do you think? > > > On Wed, May 9, 2012 at 3:04 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > >> Checking file md.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 0.000 >> # Atoms 2569 >> Last frame 2000 time 100000.000 >> >> >> Item #frames Timestep (ps) >> Step 2001 50 >> Time 2001 50 >> Lambda 2001 50 >> Coords 0 >> Velocities 2001 50 >> Forces 0 >> Box 2001 50 >> >> Well, it looks ok. Any suggestions? >> >> >> On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo <j...@um.es> wrote: >> >>> Sorry, I saw now the command line you've posted. Did you check your trr >>> with gmxcheck? >>> >>> >>> El 09/05/12 15:49, Steven Neumann escribió: >>> >>> hello gmx users, >>> >>> >>> I am sorry for bothering you but I was searching mailing list and no >>> results. I have a problem with my test particle insertion as I run the >>> workflow I described previously with my mdp: >>> >>> title = Test Particle Insertion >>> ; Run parameters >>> integrator = tpi >>> nsteps = 50000000 ; 100 ns >>> dt = 0.002 ; 2 fs >>> ; Output control >>> nstxout = 0 ; suppress .trr output ; output coordinates >>> every 25 ps >>> nstvout = 25000 ; velocities to output every 25000 steps >>> nstenergy = 1000 ; save energies every 2 ps >>> nstlog = 1000 ; update log file every 2 ps >>> nstxtcout = 100000 ; suppress (tlumic) xtc trajectory >>> energygrps = System >>> continuation = no ; first dynamics run >>> constraint_algorithm = lincs ; holonomic constraints >>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >>> constrained >>> lincs_iter = 1 ; accuracy of LINCS >>> lincs_order = 4 ; also related to accuracy >>> ; Neighborsearching >>> ns_type = grid ; search neighboring grid cells >>> nstlist = 5 ; 10 fs >>> vdwtype = Switch >>> rvdw-switch = 1.0 >>> rlist = 1.4 ; short-range neighborlist cutoff (in nm) >>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) >>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm) >>> ewald_rtol = 1e-5 ; relative strenght of the Ewald-shifted >>> potential rcoulomb >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.12 ; grid spacing for FFT >>> ; Temperature coupling is on >>> tcoupl = V-rescale ; modified Berendsen >>> thermostat >>> tc_grps = System ; two coupling groups - more >>> accurate >>> tau_t = 0.1 ; time constant, in ps >>> ref_t = 318 ; reference temperature, one >>> for each group, in K >>> ; Pressure coupling is on >>> pcoupl = Parrinello-Rahman ; pressure coupling is on >>> for NPT >>> pcoupltype = isotropic ; uniform scaling of box >>> vectors >>> tau_p = 2.0 ; time constant, in ps >>> ref_p = 1.0 ; reference pressure, in bar >>> compressibility = 4.5e-5 ; isothermal compressibility >>> of water, bar^-1 >>> ; Periodic boundary conditions >>> pbc = xyz ; 3-D PBC >>> ; Dispersion correction >>> DispCorr = EnerPres ; account for cut-off vdW scheme >>> ; Velocity generation >>> gen_vel = yes ; assign velocities from Maxwell distribution >>> gen_temp = 318 ; temperature for Maxwell distribution >>> gen_seed = -1 ; generate a random seed >>> >>> Then My log file: >>> >>> >>> The temperature for test particle insertion is 318.000 K >>> >>> Started Test Particle Insertion on node 0 Wed May 9 14:18:18 2012 >>> >>> Will insert 3 atoms with partial charges >>> >>> Will insert 50000000 times in each frame of md318.trr >>> Will use the same neighborlist for 5 insertions in a sphere of radius >>> 0.050000 >>> >>> <V> = -nan nm^3 >>> <mu> = -nan kJ/mol >>> No MEGA Flopsen this time >>> >>> R E A L C Y C L E A N D T I M E A C C O U N T I N G >>> >>> Computing: Nodes Number G-Cycles Seconds % >>> ------------------------------ >>> ----------------------------------------- >>> Rest 4 5.218 1.9 100.0 >>> ----------------------------------------------------------------------- >>> Total 4 5.218 1.9 100.0 >>> ----------------------------------------------------------------------- >>> >>> Parallel run - timing based on wallclock. >>> >>> NODE (s) Real (s) (%) >>> Time: 0.485 0.485 100.0 >>> (Mnbf/s) (MFlops) (steps/hour) >>> Performance: 0.000 0.000 0.0 >>> Finished mdrun on node 0 Wed May 9 14:18:19 2012 >>> >>> >>> >>> Files are empty. Do you have any clue what is happening? >>> >>> Thank you for your time, >>> >>> Steven >>> >>> >>> On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <j...@um.es> wrote: >>> >>>> Hi Steven >>>> >>>> As I remember, TPI is based on the calculation of the potential at >>>> every conformation from the already computed simulation (inserting the >>>> particle in every snapshot), so velocities are not used. >>>> >>>> Anyway, use both and see if there are any differences. >>>> >>>> Javier >>>> >>>> El 09/05/12 11:27, Steven Neumann escribió: >>>> >>>> Dear Gmx Users, >>>> >>>> I am running TPI of the water in the system containing free amino >>>> acids. Steps: >>>> >>>> 1. I run the NPT simulation of 100 ns to equilibrate the system. >>>> 2. I added 1 extra water molecule to the final pdb file (converted from >>>> gro) and to topology >>>> 3. I creaded tpi.tpr using grompp using new pdb file with extra water >>>> molecule >>>> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg >>>> -tpid tpid298.xvg >>>> >>>> My question: Is it better generate new velocities in my mdp file >>>> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use >>>> velocities from previous simulations (gro file)? >>>> If the second option is more appropriate what velocity shall I adjust >>>> to the extra water molecule? >>>> >>>> I will appreciate your reply. >>>> >>>> Steven >>>> >>>> >>>> >>>> -- >>>> Javier CEREZO BASTIDA >>>> PhD Student >>>> Physical Chemistry >>>> Universidad de Murcia >>>> Murcia (Spain) >>>> Tel: (+34)868887434 >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> >>> >>> -- >>> Javier CEREZO BASTIDA >>> PhD Student >>> Physical Chemistry >>> Universidad de Murcia >>> Murcia (Spain) >>> Tel: (+34)868887434 >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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