[gmx-users] Re: gmx-users Digest, Vol 58, Issue 61
Re Benchmarks, Fixed! After making all the changes that Justin suggested the dynamics run as expected, if anyone wants the scripts to run the exact same system then I am happy to send them on. Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 58, Issue 59
> Robert Fenwick wrote: >> Hi, >> >> I wanted to run one of the gromacs 4.0 benchmarks on a new cluster >> that we have and also wanted to see the affect of this 4 fs time step. >> If it would not be too much trouble would it be possible for the >> setups of either the PLINCS paper or the GROMACS 4.0 paper to be >> placed somewhere on the website. Specifically I am intersted in the >> lysozyme benchmark, however I suspect others might like the membrane >> system to as well. >> >> I have tried to set a similar simulation up, but it is not able to run >> with 4 fs integration. >> > > So what exactly is going wrong? What is in your .mdp file? It is probably > better for you to post this information here and receive feedback, so that > others can make use of it later. I've followed what I think is a sensible setup, which comes from the GROMACS workshop pre-workshop tutorial. Comments are wellcome, I generate this using a bash script for convenience: grep -v HOH original/1LYD.pdb > ./prot1LYD.pdb pdb2gmx -f prot1LYD.pdb -ter -ignh -vsite hydrogens -water tip3p select OPLS, 0, 0 editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o sol.tpr genion -s sol.tpr -nn 8 -nname CL- -nq -1 -np 0 -pname NA+ -pq 1 -p topol.top -o solvatedIon.gro select 12 (SOL) grompp -f em.mdp -p topol.top -c solvatedIon.gro -o em.tpr mdrun -v -deffnm em grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr mpirun -np 16 mdrun_mpi -v -deffnm pr -npme 8 grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr mpirun -np 16 mdrun_mpi -v -deffnm run -npme 8 The inputs are, and come directly from the article Hess et al., 2008 JCTC GROMACS 4 : :: em.mdp :: integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 nstenergy = 10 :: pr.mdp :: integrator = md nsteps = 5 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 Pcoupl = Berendsen tau-p = 1.0 compressibility = 1e-5 1e-5 1e-5 0 0 0 ref-p = 1.0 nstenergy = 100 define = -DPOSRES :: run.mdp :: integrator = md nsteps = 5 dt = 0.004 nstlist = 5 rlist = 1.0 coulombtype = pme fourierspacing = 0.125 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 lincs-order = 6 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstenergy = 100 The simulation dies with: Step 6, time 0.024 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.222533, max 1.229818 (between atoms 328 and 329) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1970 1973 90.00.2413 0.3543 0.1930 1888 1891 65.80.4413 0.1879 0.1930 447449 59.20.2406 0.1939 0.1939 656660 90.00.1930 0.4267 0.1930 616619 90.00.1924 0.2612 0.1930 477480 89.90.2945 0.3802 0.1930 319329 65.30.1670 0.1816 0.1670 328329 90.00.0915 0.2039 0.0915 762765 42.40.1584 0.1554 0.1583 762766 44.00.1581 0.1616 0.1583 t = 0.024 ps: Water molecule starting at atom 16419 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 949 and 963 at distance 6.212 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 747 and 753 at distance 14.118 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size --- Program mdrun_mpi, VERSION 4.0.3 Source code file: pme.c, line: 518 Fatal error: 11 particles communicated
[gmx-users] Gromacs 4.0 Benchmarks
Hi, I wanted to run one of the gromacs 4.0 benchmarks on a new cluster that we have and also wanted to see the affect of this 4 fs time step. If it would not be too much trouble would it be possible for the setups of either the PLINCS paper or the GROMACS 4.0 paper to be placed somewhere on the website. Specifically I am intersted in the lysozyme benchmark, however I suspect others might like the membrane system to as well. I have tried to set a similar simulation up, but it is not able to run with 4 fs integration. Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] energy and coordinates at different times
Dear All, I am starting some simulations and would like to write out some coordinates more frequently than others, is this currently possible. Below is how I envisaged using the commands, however it seems that I don't quite understand. Is something like this possible and how do I implement this? Cheers, Bryn nstxtcout = 1000 50 1 nstenergy = 1000 50 1 xtc_grps= System Protein N_H energygrps = System Protein N_H ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Water molecule can not be settled
Hi,
My simulation has fall over with this error:
t = 501.346 ps: Water molecule starting at atom 8367 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files
with previous
and current coordinates
What can I do to fix it? There are a few other that have had this
problem on the list, but none are using 3.3.3 or have posted the
solution.
Bryn
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 2500
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 100
nstxout = 10
nstvout = 10
nstfout = 0
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 39
nky = 39
nkz = 39
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
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 = 0.8333
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
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: 2585.45 11571.5
ref_t:298 298
tau_t:0.1 0.1
anneal: No No
ann_npoints: 0 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= 2789, targetcg= 1394, myshift=0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 2790
nsb->natoms: 8576
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 085762790 2790
Max number of connections per atom is 58
Total number of connections is 34155
Max number of graph edges per atom is 4
Total number of graph edges is 13304
Table routines are used for coulomb: TRUE
Table routines are used fo
[gmx-users] normal mode analysis
Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the protein:ligand eigenvec_b.trr to the protein by issuing; > trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr > select 0 [System] Where: + nm_a.tpr is the tpr file of the protein alone + eigenvec_b.trr is the trajectory of the protein:ligand + eigenvec_c.trr is the new trajectory of the complex minus the ligand coordinates What I want to do now is compare the eigenvec_a.trr and eigenvec_c.trr files to see the mode overlap between the free and bound protein. What I can not understand how to remove the effects of rotation and translation of the protein with respect to the ligand that will be present in the eigenvec_c.trr. Is it possible to do this type of analysis in GROMACS and how can I go about it? Regards, Bryn == R. Bryn FenwickDepartment of Biochemistry, [EMAIL PROTECTED]University of Cambridge, [EMAIL PROTECTED]80 Tennis Court Road, Tel: +44 1223 766018 Old Addenbrookes Site, Fax: +44 1223 766002 Cambridge, CB2 1GA, UK. == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] GTP topology
Here are the topology file lines that I have added to my version of ffG43a1.rtp It should just work if you add these lines to this file. If anyone has any comments then I would be happy to have them, this is the first time I have done this. Bryn [ GTP ] [ atoms ] GN9NR-0.2 0 GC4 C 0.2 0 GN3NR-0.36000 1 GC2 C 0.36000 1 GN2NT-0.83000 2 GH21 H 0.41500 2 GH22 H 0.41500 2 GN1NR-0.28000 3 GH1 H 0.28000 3 GC6 C 0.38000 4 GO6 O-0.38000 4 GC5 C 0.0 5 GN7NR-0.36000 5 GC8 CR1 0.36000 5 GC2* CH1 0.15000 6 GO2*OA-0.54800 6 GH2* H 0.39800 6 GC3* CH1 0.15000 7 ; like ATP set to GC2* GO3*OA-0.54800 7 ; like ATP set to GO2* GH3* H 0.39800 7 ; like ATP set to GH2* GC1* CH1 0.2 8 GC4* CH1 0.16000 8 GO4*OA-0.36000 8 GC5* CH2 0.0 9 GO5*OA-0.3600010 GPA P 0.7050010 ; from ATP GO1PAOM-0.6350010 ; from ATP GO2PAOM-0.6350010 ; from ATP GO3PAOA-0.3600011 ; from ATP GPB P 0.7050011 ; from ATP GO1PBOM-0.6350011 ; from ATP GO2PBOM-0.6350011 ; from ATP GO3PBOA-0.3600012 ; from ATP GPG P 0.6300012 ; from ATP GO1PGOM-0.6350012 ; from ATP GO2PGOM-0.6350012 ; from ATP GO3PGOA-0.5480012 ; from ATP GH3PG H 0.3980012 ; from ATP [ bonds ] GO5* GC5*gb_19 GC5* GC4*gb_25 GC4* GO4*gb_19 GC4* GC3*gb_25 GO4* GC1*gb_19 GC1* GN9gb_21 GC1* GC2*gb_25 GN9 GC4gb_9 GN9 GC8gb_9 GC4 GN3gb_11 GC4 GC5gb_15 GN3 GC2gb_11 GC2 GN2gb_8 GC2 GN1gb_16 GN2 GH21gb_2 GN2 GH22gb_2 GN1 GH1gb_2 GN1 GC6gb_16 GC6 GO6gb_4 GC6 GC5gb_15 GC5 GN7gb_9 GN7 GC8gb_9 GC2* GO2*gb_19 GO2* GH2*gb_1 GC2* GC3*gb_25 GC3* GO3*gb_19 ; like ATP set to GC2* GO3* GH3*gb_1; like ATP set to GO2* GO5* GPAgb_27 ; from ATP GPA GO1PAgb_23 ; from ATP GPA GO2PAgb_23 ; from ATP GPA GO3PAgb_27 ; from ATP GO3PA GPBgb_27 ; from ATP GPB GO1PBgb_23 ; from ATP GPB GO2PBgb_23 ; from ATP GPB GO3PBgb_27 ; from ATP GO3PB GPGgb_27 ; from ATP GPG GO1PGgb_23 ; from ATP GPG GO2PGgb_23 ; from ATP GPG GO3PGgb_27 ; from ATP GO3PG GH3PGgb_1; from ATP [ exclusions ] ; aiaj GC1* GN3 GC1* GC5 GC1* GN7 GN9 GC2 GN9 GC6 GC4 GN2 GC4 GN1 GC4 GO6 GN3 GH1 GN3 GC6 GN3 GN7 GN3 GC8 GC2 GO6 GC2 GC5 GN2 GH1 GN2 GC6 GN1 GN7 GH1 GO6 GH1 GC5 GC6 GC8 GO6 GN7 GO3PB GH3PG ; from ATP GO1PG GH3PG ; from ATP GO2PG GH3PG ; from ATP [ angles ] ; aiajak gromos type GO5* GC5* GC4* ga_8 GC5* GC4* GO4* ga_8 GC5* GC4* GC3* ga_7 GO4* GC4* GC3* ga_8 GC4* GO4* GC1* ga_9 GO4* GC1* GN9 ga_8 GO4* GC1* GC2* ga_8 GN9 GC1* GC2* ga_8 GC1* GN9 GC4 ga_36 GC1* GN9 GC8 ga_36 GC4 GN9 GC8 ga_6 GN9 GC4 GN3 ga_38 GN9 GC4 GC5 ga_6 GN3 GC4 GC5 ga_26 GC4 GN3 GC2 ga_26 GN3 GC2 GN2 ga_26 GN3 GC2 GN1 ga_26 GN2 GC2 GN1 ga_26 GC2 GN2 GH21 ga_22 GC2 GN2 GH22 ga_22 GH21 GN2 GH22 ga_23 GC2 GN1 GH1 ga_24 GC2 GN1 GC6 ga_26 GH1 GN1 GC6 ga_24 GN1 GC6 GO6 ga_26 GN1 GC6 GC5 ga_26 GO6 GC6 GC5 ga_26 GC4 GC5 GC6 ga_26 GC4 GC5 GN7 ga_6 GC6 GC5 GN7 ga_38 GC5 GN7 GC8 ga_6 GN9 GC8 GN7 ga_6 GC1* GC2* GC3* ga_7 GC1* GC2* GO2* ga_8 GO2* GC2* GC3* ga_8 GC2* GO2* GH2* ga_11 GC3* GO3* GH3* ga_11 ; like ATP set to GC2* GC4* GC3* GC2* ga_7 GC4* GC3* GO3* ga_8 GC2* GC3* GO3* ga_8 GC5* GO5* GPA ga_25 ; from ATP GO5* GPA GO1PA ga_13 ; from ATP GO5* GPA GO2PA ga_13 ; from ATP GO5* GPA GO3PA ga_4; from ATP GO1PA GPA GO2PA ga_28 ; from ATP GO1PA GPA GO3PA ga_13 ; from ATP GO2PA GPA GO3PA ga_13 ; from ATP GPA GO3PA GPB ga_25 ; from ATP GO3PA GPB GO1PB ga_13 ; from ATP GO3PA GPB GO2PB ga_13 ; from ATP GO3PA GPB GO3PB ga_4; from ATP GO1PB GPB GO2PB ga_28 ; from ATP GO1PB GPB GO3PB ga_13 ; from ATP GO2PB GPB GO3PB ga_13 ; from ATP GPB GO3PB GPG ga_25 ; from ATP GO3PB GPG GO1PG ga_13 ; from ATP GO3PB GPG GO2PG ga_13 ; from ATP GO3PB GPG GO3PG ga_4; from ATP GO1PG GPG GO2PG ga_28 ; from ATP GO1PG
[gmx-users] GTP topology file for ffG43a1
Dear all, I have now prepared what I think are the necessary lines for entry into the ffG43a1.rtp file for GTP, however I was wanting a quick way to test what I have done. Again I am open to suggestions. Specifically I want to ensure that I have added sufficient bonds and angles for the molecule and that I have not defined any of the parameters more than once. I am quite happy to send on my files, if someone would like to help, basically my approach has been to cannibalise the ATP, AED and GUA files. Is there a simple way to produce a .gro or .pdb file from my altered ffG43a1.rtp? Cheers, Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] ATP, GTP and REX
Hi, I would like to make some unrestrained simulations of ATP and GTP binding proteins and wondered if there were any topology files floating about for OPLSAA or the GROMOS96.1 forcefields for these two ligands? I understand that the gmx forcefields have been deprecated and that I should use one of the newer ones, however there are not that many ligand topology files about. I am just starting out, so any suggestions would be welcome. The systems are approximately 300 residues in size and I am interested in the stability and rms fluctuations of the systems. A secondary question is that of the AMBER forcefields, I am using the 3.3.2 version, however the amber files state specifically to use the port for the relevant version, one of which is missing for 3.3.2. Is it safe to use the 3.3.1 amber ff port with version 3.3.2 of GROMACS? Finally, if anyone can point me in the direction of a small test project that does some simple replica exchange, with some instructions as to how to get it to run, I would be very grateful. Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
