[gmx-users] Range Checking error
Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file: nsgrid.c, line: 226 // // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot // put these on a grid, so this is usually where we detect those errors. // Make sure your system is properly energy-minimized and that the potential // energy seems reasonable before trying again. /Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00 bonds that rotated more than 30 degrees: also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav / // Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] // Please report this to the mailing list (gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users) // --- // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // http://www.gromacs.org/mailman/listinfo/gmx-users // Please don't post (un)subscribe requests to the list. Use the www // interface or send it to gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se http://www.gromacs.org/mailman/listinfo/gmx-users spoel at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How 2 remove these warnings
Hi, I am getting these two warnings while doing the pdb2gmx steps.Please give some suggestions on this problem. WARNING 1 [file AFA.top, line 350]: No default Ryckaert-Bell. types, using zeroes WARNING 2 [file AFA.top, line 455]: No default Ryckaert-Bell. types, using zeroes Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 1480 processing coordinates... double-checking input for internal consistency Regards, Richa __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How 2 remove these warnings
Check the line as specified in the warning. And translate the atom number to its atom type. Check such combination in the [dihedral] section in the ffX-nb.itp whether there is such combination. I suspect that there is some mis-naming by pdb2gmx. Check the total charge of the molecule as well, it shall be a integer. Yang Ye Richa taimni wrote: Hi, I am getting these two warnings while doing the pdb2gmx steps.Please give some suggestions on this problem. WARNING 1 [file AFA.top, line 350]: No default Ryckaert-Bell. types, using zeroes WARNING 2 [file AFA.top, line 455]: No default Ryckaert-Bell. types, using zeroes Excluding 3 bonded neighbours for Protein 1 Excluding 2 bonded neighbours for SOL 1480 processing coordinates... double-checking input for internal consistency Regards, Richa __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS Warning using mdrun
Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Range Checking Error
//
// Range checking error:
// Explanation: During neighborsearching, we assign each particle to a grid
// based on its coordinates. If your system contains collisions or parameter
// errors that give particles very high velocities you might end up with some
// coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// put these on a grid, so this is usually where we detect those errors.
// Make sure your system is properly energy-minimized and that the potential
// energy seems reasonable before trying again.
/Please follow the advice in the above two sentences. Check your structure.
I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 24594
Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps=1
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
I get the following
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00
bonds that rotated more than 30 degrees:
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy = 250
nstxtcout = 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = TRUE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 20
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed = 815131
rlist = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[ 2]={ 0.0e+00, 0.0e+00, 0.0e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 51456
ref_t: 300
tau_t: 1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
CPU= 0, lastcg= 8223, targetcg= 4112, myshift= 0
nsb-shift = 1, nsb-bshift= 0
Neighbor Search Blocks
nsb-nodeid: 0
nsb-nnodes: 1
nsb-cgtotal: 8224
nsb-natoms: 24594
nsb-shift: 1
nsb-bshift: 0
Nodeid index homenr cgload workload
0 0 24594 8224 8224
Max number of graph edges per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm
[gmx-users] Range Checking Error
/ //
// // Range checking error:
// // Explanation: During neighborsearching, we assign each particle to a grid
// // based on its coordinates. If your system contains collisions or
parameter
// // errors that give particles very high velocities you might end up with
some
// // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
// // put these on a grid, so this is usually where we detect those errors.
// // Make sure your system is properly energy-minimized and that the
potential
// // energy seems reasonable before trying again.
// /Please follow the advice in the above two sentences. Check your structure.
//
// I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
// and steep using -DFLEXIBLE in my mdp file and I was able to compute using
mdrun but I got the following in my log file
//
// Initiating Steepest Descents
// Center of mass motion removal mode is Linear
// We have the following groups for center of mass motion removal:
// 0: rest, initial mass: 24594
// Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
// Removing pbc first time
// Done rmpbc
// Steepest Descents:
//Tolerance (Fmax) = 1.0e+01
//Number of steps=1
// Grid: 10 x 10 x 20 cells
// Configuring nonbonded kernels...
// Testing AMD 3DNow support... not present.
// Testing ia32 SSE support... present.
//
//
// Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
// I get the following
//
// Step 0, time 0 (ps) LINCS WARNING
// relative constraint deviation after LINCS:
// max 1391229833052160.00 (between atoms 655 and 657) rms
40665803128832.00
// bonds that rotated more than 30 degrees:
/
turn off the constraints
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
---
Input Parameters:
integrator = md
nsteps = 1000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 1
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy= 250
nstxtcout= 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= TRUE
bShakeSOR= FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p= 20
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
andersen_seed= 815131
rlist= 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout = 100
orires_fc= 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau= 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter= 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake_tol= 1e-04
lincs_order =
Re: [gmx-users] Range Checking Error
Gaurav Chopra wrote: Gaurav Chopra wrote: / Hi // // I am doing a steepest descent for the initial mdrun for a peptide and it // gives me the following error. Please advice. // // Thanks // Gaurav // --- // Program mdrun, VERSION 3.3 // Source code file: nsgrid.c, line: 226 // // Range checking error: // Explanation: During neighborsearching, we assign each particle to a grid // based on its coordinates. If your system contains collisions or parameter // errors that give particles very high velocities you might end up with some // coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot // put these on a grid, so this is usually where we detect those errors. // Make sure your system is properly energy-minimized and that the potential // energy seems reasonable before trying again. /Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=1 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.00 (between atoms 655 and 657) rms 40665803128832.00 bonds that rotated more than 30 degrees: turn off the constraints also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav / // Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] // Please report this to the mailing list (gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users) // --- // // ___ // gmx-users mailing listgmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users // http://www.gromacs.org/mailman/listinfo/gmx-users // Please don't post (un)subscribe requests to the list. Use the www // interface or send it to gmx-users-request at gromacs.org. http://www.gromacs.org/mailman/listinfo/gmx-users // Can't post? Read http://www.gromacs.org/mailing_lists/users.php / -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se http://www.gromacs.org/mailman/listinfo/gmx-users spoel at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 starting mdrun 'HEADER Output set 125 with rmsf= .982 of 1nkd.cl_nH_tir.pdb in water' 10 steps,200.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: Thanks gaurav ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] LINCS Warning using mdrun
Gaurav Chopra wrote: Hi I get the following error when using mdrun for a protein in solution. I have checked the structure and everything looks fine to me. Could you suggested anything else I could do. How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: LINCS Warning using mdrun
/ Hi // // I get the following error when using mdrun for a protein in solution. // I have checked the structure and everything looks fine to me. Could // you suggested anything else I could do. / How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen --- Hi I used the initial minimization run using grompp and mdrun using steepest descent for 400 steps and 0.002 ps as the step size. The constraints are all-atom. The following is the output from the log file that was generated after the md. Any suggestions? Thanks Gaurav --- mdrun log file output -- Initializing LINear Constraint Solver number of constraints is 934 average number of constraints coupled to one constraint is 3.6 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.608377894898 0.031756 After LINCS 0.126305892894 0.007000 Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.126305 (between atoms 892 and 894) rms 0.007000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 898899 41.60.1015 0.0997 0.1010 898900 38.10.1038 0.0984 0.1010 Going to use C-settle (6845 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074 rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.115310685686 0.023558 After LINCS 0.115624892894 0.006694 Started mdrun on node 0 Tue Mar 14 04:21:35 2006 Initial temperature: 299.541 K Step Time Lambda 00.00.0 Grid: 12 x 12 x 12 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. There are 21469 atoms in your xtc output selection Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 10.170899898899 0.711794 After LINCS 3.372058894895 0.239340 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 3.372058 (between atoms 894 and 895) rms 0.239340 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 883886 36.70.1540 0.2007 0.1529 886887 36.80.1098 0.1474 0.1090 886888 43.60.1099 0.1575 0.1090 886889 51.70.1526 0.2510 0.1529 889890 60.60.1097 0.1917 0.1090 889891 66.20.1096 0.2043 0.1090 889892 44.60.1561 0.0485 0.1463 892893 55.70.1042 0.1304 0.1010 894895 54.60.1221 0.5859 0.1340 894898 135.90.1495 0.4473 0.1340 895896 77.60.1051 0.0671 0.1010 895897 40.40.1011 0.1018 0.1010 898899 40.00.0997 0.3249 0.1010 903905 40.20.1453 0.1959 0.1449 905906 45.20.1093 0.1556 0.1090 905907 65.60.1542 0.3041 0.1529 905921 35.00.1527 0.1990 0.1522 907908 83.40.1099 0.2156 0.1090 907909 70.10.1099 0.1907 0.1090 907910 43.60.1519 0.1400 0.1510 910911 77.90.1408 0.3459 0.1400 910913 77.50.1407 0.3356 0.1400 911912 80.80.1084 0.2512 0.1080 911915 74.90.1405 0.2010 0.1400 913914 81.80.1084 0.2760 0.1080 913917 65.80.1404 0.1278 0.1400 915916 81.70.1082 0.2186 0.1080 915919 41.00.1402 0.1786 0.1400 917918 82.90.1082 0.2569 0.1080 917919 32.70.1402 0.1652 0.1400 919920 82.30.1082 0.1984 0.1080 Constraint error in algorithm Lincs at step 0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 2.38010e+034.15026e+018.53343e+021.45562e+034.52843e+03 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.78128e+05 -3.41925e+05
Re: [gmx-users] xtc files
Thanks David, That works! On Tue, 14 Mar 2006 08:49:43 +0100, David van der Spoel wrote: YOLANDA SMALL wrote: Hi All, How do I convert xtc files exported for a subset of atoms in my system to pdb files? When I run trjconv, I get the following error message: Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory file (3152) In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and protein atoms to an xtc file. This subset of atoms is defined in my index file and contains 3152 atoms. Then I discard the .trr files to save space. It looks like the atom index gets renumbered from 1 in the new .xtc file so that the new atom indeces no longer correspond to the atoms in the original coordinate file. How do I recover the coordinates with matching atom names from the .xtc file? Sorry I misread your question. You make a pdb file from your original tpr using the same index group you used for the xtc-grps, then you use this pdb file as reference for trjconv on the xtc to pdb conversion. Thanks, Yolanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: LINCS Warning using mdrun
Gaurav Chopra wrote: / Hi // // I get the following error when using mdrun for a protein in solution. // I have checked the structure and everything looks fine to me. Could // you suggested anything else I could do. / How did you energy minimze your structure? What was the output of mdrun during energy minization, especially the last line with Fmax, Epot etc.? I should look like this: Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05, atom= 78754 Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03, atom= 13032 Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04, atom= 13032 Jochen Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen --- Hi I used the initial minimization run using grompp and mdrun using steepest descent for 400 steps and 0.002 ps as the step size. The constraints are all-atom. The following is the output from the log file that was generated after the md. Any suggestions? Thanks Gaurav --- mdrun log file output -- Better show us the output of your energy minimization. The ouput of your md only shows that your sctructure has some serious problem...like your box is too small or whatever... Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pull.pdo AFM force
Hi all I have a short question. Could you please tell me what do the columns in pull.pdo (output file from AFM) stand for. Is there a simple way to obtain forces from AFM pulling? Thank you for help. Michal As an example, with one pulling group, and pulling in 3D, the output columns read: Time, Reference group X, Reference group Y, Reference group Z, Pull Group X, Pull Group Y, Pull Group Z, Spring X, Spring Y, Spring Z for a total of 10 columns. If you didn't pull in 3D, you'll only get output for the dimensions where pulldim was set to Y in your .ppa file. I'm not sure how multiple pull groups are handled. I have a script to calculate the forces for pull runs using only one pull group in 3 dimensions that I can share on request. -Emily Walton ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
