[gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step
Respected Sir, I am working with gromacs and i have got a warning as shown below.Can you please suggest me what to do, to run my file completely.Please reply as soon as possible.Awaiting your suggestions. Step Time Lambda 00.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.03693e+039.37838e+021.75330e+021.49262e+031.26876e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.90866e+06 -4.76268e+03 -1.13536e+066.29348e+03 -9.65761e+03 PotentialKinetic En. Total EnergyTemperature Pressure (bar) 3.78150e+062.48247e+102.48284e+104.18046e+073.81032e+08 Constr. rmsd 3.57946e+01 Step 1 Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step -- View this message in context: http://gromacs.5086.x6.nabble.com/Warning-pressure-scaling-more-than-1-mu-58-1548-58-1548-58-1548-Received-the-TERM-signal-stopping-atp-tp5015412.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step
Your starting configuration has positions that cause aims to overlap, causing huge LJ energies. Fix that. Mark On Mar 27, 2014 7:43 AM, Lakshmi lpgold...@gmail.com wrote: Respected Sir, I am working with gromacs and i have got a warning as shown below.Can you please suggest me what to do, to run my file completely.Please reply as soon as possible.Awaiting your suggestions. Step Time Lambda 00.00.0 Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 1.03693e+039.37838e+021.75330e+021.49262e+031.26876e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 4.90866e+06 -4.76268e+03 -1.13536e+066.29348e+03 -9.65761e+03 PotentialKinetic En. Total EnergyTemperature Pressure (bar) 3.78150e+062.48247e+102.48284e+104.18046e+073.81032e+08 Constr. rmsd 3.57946e+01 Step 1 Warning: pressure scaling more than 1%, mu: 58.1548 58.1548 58.1548 Received the TERM signal, stopping at the next NS step -- View this message in context: http://gromacs.5086.x6.nabble.com/Warning-pressure-scaling-more-than-1-mu-58-1548-58-1548-58-1548-Received-the-TERM-signal-stopping-atp-tp5015412.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_select
Hello, for the PME gromacs was giving me warnings about PME load so I putted that values to fix warnings. I did not know this could affect accuracy. For the .ndx file, actually I was supplying select.ndx and it can be seen in previous mail. I was trying to put both select.ndx and index.ndx in -n flag but it is not possible so I need to put it both in one .ndx file. Thank you very much, you deserve chocolate :-). 2014-03-26 18:38 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 3/26/14, 11:57 AM, Josip Lovrić wrote: Thank you for the tips! This is my .mdp file: title = nacl ; Run parameters integrator = md ; leap-frog integrator nsteps = 200 ; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = no ; Restarting after NPT 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 rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.6 ; grid spacing for FFT Are you sure this is the value you want? Your PME grid is going to be about 5x coarser than the default settings, so your run will be much faster, but less accurate... ; 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 = 335 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen;Parrinello-Rahman ; Pressure coupling on in 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-6 ; isothermal compressibility of NaCl, 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 = 335 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed energygrps = Na Cl MOL notattached Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 16800 1 16800 1 Ion 5600 15600 2 Na 2800 12800 3 Cl 280028015600 4 MOL112005601 16800 5 Other 112005601 16800 6 Na 2800 12800 7 Cl 280028015600 8 MOL112005601 16800 Contents of index file select.ndx -- Nr. Group #Entries FirstLast 0 notattached_0.000 30505901 16800 You can't use groups across two index files. I assume you are supplying index.ndx to grompp (showing the actual command you're using helps), which leaves notattached out in the cold and undefined. You need all necessary index groups in a single index file. -Justin 2014-03-26 16:36 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 3/26/14, 11:30 AM, Josip Lovrić wrote: Hello, I managed to create notattached group but now it is not recognizing system group when I compile it with gromp. I get this answer: Fatal error: Group system referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. This is my grompp line: grompp_mpi -f md.mdp -c nacl_palm_md_224.gro -p topol_nc.top -o nacl_palm_md_224_na.tpr -n select.ndx group system is defined like this in .top file: [ system ] ; Name NaCl P.S. Feel free to ask me more information, I am quite new in gromacs and I am not sure if I am giving you all the information. The [system] directive just gives a name for output coordinate files and such. It is not equivalent to the System index group. When reporting errors with groups, index files, etc, you need to provide the text of the .mdp file and, at minimum, a listing of the groups in the index file, e.g. from gmxcheck. -Justin --
[gmx-users] Coulomb and Lennnard-Jones parameters
Dear Gromacs users
I would like to ask for your advice concerning to the input parameters for
a simulation. I am simulating a protein (1L2Y,
http://www.rcsb.org/pdb/explore/explore.do?structureId=1L2Y). I obtain the
timing results below.
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-CyclesSeconds %
---
Comm. coord. 8 11 198.994 58.7 1.0
Neighbor search8 20001 1402.166 413.3 7.3
Force8 1110529.644 3103.954.6
Wait + Comm. F 8 11 331.925 97.8 1.7
PME mesh 8 11 6183.435 1822.8 32.0
Write traj. 81013.4341.0
0.0
Update 8 11 148.251 43.7 0.8
Constraints 8 11 304.236 89.7 1.6
Comm. energies 8 20002 36.774 10.8 0.2
Rest 8 162.448 47.9
0.8
---
Total 8 19301.307 5689.7
100.0
---
---
PME redist. X/F8 22 3957.969 1166.720.5
PME spread/gather 8 22 1502.640 443.0 7.8
PME 3D-FFT 8 22 477.460 140.7 2.5
PME solve 8 11 242.220 71.4 1.3
---
Parallel run - timing based on wallclock.
I was expecting the constraint time to take above 15% of the total time.
However, I find just 1.6%. I suspect that perhaps the parameters for the
Coulomb and Lennnard-Jones calculation may be improved: In the md.log file,
I find:
Computing:M-Number M-Flops
% Flops
-
Coul(T) + LJ [W3-W3] 18217.759964 6959184.30676.8
Is this wise? May you give me a hint on how to tune the parameters?
These are my input parameters:
integrator = md
nsteps = 10
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstcalcenergy= 5
nstenergy= 1000
nstxtcout= 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 28
nky = 28
nkz = 28
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= TRUE
bShakeSOR= FALSE
etc = V-rescale
nsttcouple = 5
epc = Parrinello-Rahman
epctype = Isotropic
nstpcouple = 5
tau_p= 2
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}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rlistlong= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 1
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.05016
Re: [gmx-users] compilation error with gcc in non-standard location
thanks for both replies ... -DGMX_CPU_ACCELERATION=SSE2 did the trick ... regards michael -- View this message in context: http://gromacs.5086.x6.nabble.com/compilation-error-with-gcc-in-non-standard-location-tp5015385p5015415.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] re-sort frames by RMSD
Do you wanna sort the actual trajectory file OR just print out the sorted frame numbers? For the latter I'd use awk, python or whatever language you prefer to sort the rmsd.xvg file. The former would require a bit more work around, still, it's nothing a bit of scripting can't do. /J On Thu, Mar 27, 2014 at 12:33 PM, unitALX alec.zan...@gmail.com wrote: Hello! How can I re-sort the frames of a trajectory by increasing RMSD? -- View this message in context: http://gromacs.5086.x6.nabble.com/re-sort-frames-by-RMSD-tp5015416.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Difficulty preparing a polymer (PEG) for simulation.
I’m trying to prepare PEG for simulation in gromacs and running into considerable difficulties. My PEG chain is HOC-COC-COC…...COC-COC-COH with appropriate hydrogens on the carbons. I am using the new CHARM36.ff Following the procedure for polymers, I added a beginning, and end, and a central chain piece to ‘merged.rtp’ and modified the atom names in the .pdb file to match. I have also added the residues to the ‘residuetypes.dat’ as Non-Protein (I have also tried listing it as a Protein). pdb2gmx claims I have169 missing atoms but will create the .gro and .top files anyway with the -missing parameter passed. The .gro file has all the atoms but the .top seems to be missing much information on bonds and angles. Probably no point in continuing but after a quick editconfig, grompp gives me a fatal error: Group Protein referenced in the .mdp file was not found in the index file. I am new to gromacs and would really appreciate help getting started on its use like this. Following is some of my data files. Daniel Sponseller PhD student Computational Science and Informatics George Mason University Snip from ‘merged.rtp’ ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31 HCA2A0.090 5 H32 HCA2A0.090 6 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ] [ LIGb ] [ atoms ] OO1 OG311 -0.650 0 H11 HGP10.420 1 C3 CG3210.050 2 H31 HGA20.090 3 H32 HGA20.090 4 [ bonds ] OO1 H11 OO1C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ] [ LIGe ] [ atoms ] C1 CG3210.050 0 H11 HGA20.090 1 H12 HGA20.090 2 OO2 OG311 -0.650 3 H21 HGP10.420 4 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2 H21 my modified ‘PEG.pdb’ file: COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL HETATM1 C1 LIGe1 -14.784 -1.665 0.506 1.00 0.00 C HETATM2 C3 LIG 2 -13.927 -1.410 -0.735 1.00 0.00 C HETATM3 OO2 LIG 2 -13.056 -0.302 -0.493 1.00 0.00 O HETATM4 H11 LIGe1 -15.383 -2.563 0.355 1.00 0.00 H HETATM5 H12 LIGe1 -14.137 -1.802 1.372 1.00 0.00 H HETATM6 H31 LIG 2 -13.333 -2.297 -0.956 1.00 0.00 H HETATM7 H32 LIG 2 -14.573 -1.185 -1.584 1.00 0.00 H HETATM8 C1 LIG 2 -12.207 0.022 -1.596 1.00 0.00 C HETATM9 C3 LIG 3 -11.325 1.216 -1.227 1.00 0.00 C HETATM 10 OO2 LIG 3 -10.441 0.845 -0.167 1.00 0.00 O HETATM 11 H12 LIG 2 -11.578 -0.836 -1.835 1.00 0.00 H HETATM 12 H11 LIG 2 -12.818 0.276 -2.463 1.00 0.00 H HETATM 13 H31 LIG 3 -10.741 1.519 -2.096 1.00 0.00 H HETATM 14 H32 LIG 3 -11.953 2.046 -0.903 1.00 0.00 H HETATM 15 C1 LIG 3 -9.568 1.894 0.257 1.00 0.00 C HETATM 16 C3 LIG 4 -8.673 1.387 1.389 1.00 0.00 C HETATM 17 OO2 LIG 4 -7.815 0.358 0.894 1.00 0.00 O HETATM 18 H11 LIG 3 -8.949 2.211 -0.582 1.00 0.00 H HETATM 19 H12 LIG 3 -10.160 2.738 0.611 1.00 0.00 H HETATM 20 H31 LIG 4 -8.070 2.210 1.772 1.00 0.00 H HETATM 21 H32 LIG 4 -9.294 0.988 2.192 1.00 0.00 H HETATM 22 C1 LIG 4 -6.933 -0.187 1.877 1.00 0.00 C HETATM 23 C3 LIG 5 -6.066 -1.274 1.239 1.00 0.00 C HETATM 24 OO2 LIG 5 -5.215 -0.687 0.252 1.00 0.00 O HETATM 25 H11 LIG 4 -6.294 0.603 2.270 1.00 0.00 H HETATM 26 H12 LIG 4 -7.517 -0.619 2.690 1.00 0.00 H HETATM 27 H32 LIG 5 -5.457 -1.751 2.007 1.00 0.00 H HETATM 28 H31 LIG 5 -6.707 -2.020 0.768 1.00 0.00 H HETATM 29 C1 LIG 5 -4.360 -1.621 -0.408 1.00 0.00 C HETATM 30 C3 LIG 6 -3.499 -0.885 -1.437
Re: [gmx-users] Difficulty preparing a polymer (PEG) for simulation.
On 3/27/14, 9:54 AM, Dan Sponseller wrote: I’m trying to prepare PEG for simulation in gromacs and running into considerable difficulties. My PEG chain is HOC-COC-COC…...COC-COC-COH with appropriate hydrogens on the carbons. I am using the new CHARM36.ff Following the procedure for polymers, I added a beginning, and end, and a central chain piece to ‘merged.rtp’ and modified the atom names in the .pdb file to match. I have also added the residues to the ‘residuetypes.dat’ as Non-Protein (I have also tried listing it as a Protein). Non-Protein is not going to be recognized in residuetypes.dat. Use Other or Protein. pdb2gmx claims I have169 missing atoms but will create the .gro and .top files anyway with the -missing parameter passed. The .gro file has all the atoms but the .top seems to be missing much information on bonds and angles. Probably no point in continuing but after a quick editconfig, grompp gives me a fatal error: Group Protein referenced in the .mdp file was not found in the index file. Your input .pdb file has numerous problems. See below. I can think of only one appropriate use for -missing, and it's not here :) The fact that Protein is not found indicates you're using an .mdp file designed for simulating a protein, but your attempt to use Non-Protein above clearly contradicts any definition of the polymer as Protein. I am new to gromacs and would really appreciate help getting started on its use like this. Following is some of my data files. Daniel Sponseller PhD student Computational Science and Informatics George Mason University Snip from ‘merged.rtp’ ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31 HCA2A0.090 5 H32 HCA2A0.090 6 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ] [ LIGb ] [ atoms ] OO1 OG311 -0.650 0 H11 HGP10.420 1 C3 CG3210.050 2 H31 HGA20.090 3 H32 HGA20.090 4 [ bonds ] OO1 H11 OO1C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ] [ LIGe ] [ atoms ] C1 CG3210.050 0 H11 HGA20.090 1 H12 HGA20.090 2 OO2 OG311 -0.650 3 H21 HGP10.420 4 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2 H21 my modified ‘PEG.pdb’ file: COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL HETATM1 C1 LIGe1 -14.784 -1.665 0.506 1.00 0.00 C HETATM2 C3 LIG 2 -13.927 -1.410 -0.735 1.00 0.00 C HETATM3 OO2 LIG 2 -13.056 -0.302 -0.493 1.00 0.00 O HETATM4 H11 LIGe1 -15.383 -2.563 0.355 1.00 0.00 H HETATM5 H12 LIGe1 -14.137 -1.802 1.372 1.00 0.00 H Problem #1 - you're beginning the chain with the ending residue. In the scenario above, the chain should start (residue 1) with LIGb and end with LIGe. Problem #2 - you've got discontinuous residues. You can't start LIGe, then mix in LIG, then go back to LIGe. pdb2gmx will look at the residue numbering, and whenever it changes, it starts a new residue (i.e. its own internal numbering). Hence you're getting missing atoms in residue 1 (LIGe), because the only atom pdb2gmx finds is C1 before it encounters a new residue (LIG). -Justin HETATM6 H31 LIG 2 -13.333 -2.297 -0.956 1.00 0.00 H HETATM7 H32 LIG 2 -14.573 -1.185 -1.584 1.00 0.00 H HETATM8 C1 LIG 2 -12.207 0.022 -1.596 1.00 0.00 C HETATM9 C3 LIG 3 -11.325 1.216 -1.227 1.00 0.00 C HETATM 10 OO2 LIG 3 -10.441 0.845 -0.167 1.00 0.00 O HETATM 11 H12 LIG 2 -11.578 -0.836 -1.835 1.00 0.00 H HETATM 12 H11 LIG 2 -12.818 0.276 -2.463 1.00 0.00 H HETATM 13 H31 LIG 3 -10.741 1.519 -2.096 1.00 0.00 H HETATM 14 H32 LIG 3 -11.953 2.046 -0.903 1.00 0.00 H HETATM 15 C1 LIG 3 -9.568 1.894 0.257 1.00 0.00 C HETATM 16 C3 LIG 4 -8.673 1.387 1.389 1.00 0.00 C HETATM 17 OO2 LIG 4
[gmx-users] g_covar warnings
Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? Thank you in advance, Best regards, João Henriques -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
On 3/27/14, 1:54 PM, João Henriques wrote: Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_covar warnings
Great, that's what I needed to know. Still, I totally agree with you. There are certain best practices, and using a .tpr is always the best choice. Thanks, João On Thu, Mar 27, 2014 at 7:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:54 PM, João Henriques wrote: Thanks Justin. That corroborates my no .tpr, no party suspicion. However, would it be possible to achieve a correct analysis if I were to use a whole .gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain myself properly, but that's what I want to know. Yes, if you have removed jumps and have intact structures throughout the trajectory, you're fine. The warning is only there for users who haven't thought ahead. -Justin /J On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/14, 1:27 PM, João Henriques wrote: Hello everyone, The documentation reads: All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. This is rather cryptic, what does it mean in practice? No tpr, no party? What if I use a properly centered and whole .gro file? When ran with a .gro as the structure input file, I get two warnings. One is related to the masses, which are non-existent in the .gro, but I don't need them anyway. The second warning is honestly confusing me even more. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. The documentation points out to the structure input file and now it's the trajectory? What's going on? Do I also need to make each frame whole in the input .xtc? Can someone elaborate on this? The documentation consistently refers to the run input file. A .tpr has record of how periodicity is treated. Nothing else does. If you don't tell g_covar (like most Gromacs tools) how periodicity is treated, you can get garbage as a result. The trajectory may have broken molecules, because mdrun doesn't care how they look - it has a run input file and thus knowledge of periodicity. When running analysis like g_covar, if the bonded connectivity of the molecule and the periodicity are unknown (again, if you're not using a .tpr), then absolute displacements of coordinates are used, thus your analysis might be totally hosed if the molecule splits - that would be a rather dramatic structure change detected by g_covar. In fact, so dramatic that it's false. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Effect of a single mutation in a protein
Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
atoms of one trajectory and then projected the other trajectory on it.
I obtained the ATP parameters from a paper. Like all simulations, MD has some
limitations. So I don't want to highlight the things which may not be correct.
There is no unfolding. Also the gibbs energy surface projected on PC1 and PC2
looks quite different than RMSD vs. Rg surface calculated by g_sham (also the
lowest energy structures.)
Can I calculate del del G by TI? I am not sure how to define the reaction
coordinates. Is it a good idea to do umbrella sampling between two states to
determine the free energy?
On Thursday, 27 March 2014 8:35 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/26/14, 2:24 PM, Pappu Kumar wrote:
I have already used g_hbond. I am not sure how accurate is the H-bond
lifetime calculation. Also the trajectory snapshots need to be saved quite
often. Could you tell me how to interpret output from g_hbond -ac :
There should be references provided in the g_hbond output when calculating
lifetimes. At the very least, they're in the manual. So you can determine for
yourself how reliable the outcome is.
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
Plotting these data sets in XmGrace will clear things up.
Could you tell me how to project the configurations of the mutant simulation
on WT PC1? Are you aware of any paper where I can read more about it? Can I
compare the PC1 vs PC2 in case of WT and mutant?
See g_anaeig -h, as well as previous discussions in the list archive on doing
this.
I am trying to find out how such mutation buried inside the protein away from
the ligand binding pocket can influence the function of the protein. I
actually see some changes in the positon of the bound ATP in the mutant
compared to the WT. But I am not sure how reliable it is due to the
inaccuracies in parameterization.
Well, if your parametrization is inaccurate and you know it is, what use are
the
simulations? Or are you just wondering if there is a possibility of
inaccuracies? Either way, that's something that should be sorted out long
before doing any real simulations :)
I also calculated the Gibbs free energy landscape by g_sham using Rg and
RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with
~0 kJ/mol has changed.
Do the proteins unfold? If not, I doubt Rg vs. RMSD is a very sensitive metric
of anything. You can, of course, map back the locations of the energy minima
to
see if there are any interesting differences there, but such a plot (Rg vs.
RMSD) is probably only useful in protein (un)folding simulations.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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Re: [gmx-users] Question for bdc = xy
I think I describe it wrong. After nvt process, my box size doesn't change but, there is no separate vacuum layer, all the molecules are spread through the whole box. Just as the image shown. Do you know why does this happen? Thank you very much! On Thu, Mar 27, 2014 at 2:09 PM, ookami a meng...@vt.edu wrote: I think I describe it wrong. After nvt process, my box size doesn't change but, there is no separate vacuum layer, all the molecules are spread through the whole box. Just as the image shown. Do you know why does this happen? Thank you very much! On Fri, Mar 21, 2014 at 4:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/21/14, 4:43 PM, ookami a wrote: Hi, I just checked previous posts, they said increasing the size of z-direction to create a vaccum layer would be working. So I extend my z-direction with 3 times of the original box, when I run the pvt process, the vacuum layer disappeared. As you should expect. If you apply pressure to no resistance, it shrinks. How could I modified my nvt.mdp file? From the pre posts, seems they don't have any problem when running the nvt. Indeed, because the box is fixed. If you want commentary on your .mdp file, you'll need to post it and explain fully what the system is. Anything else is just blind guesswork, which is not productive for anyone. -Justin Thank you very much. On Fri, Mar 21, 2014 at 8:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/20/14, 11:51 PM, ookami a wrote: Dear all: I'm trying to set up a bdc only with xy, so I edited my mdp file with changing the bdc =xyz to bdc = xy. However, I got a error message which is Can not have Ewald with pbc=xy Anyone know how to solve it? Per the manual, you can't use an Ewald summation method or pressure coupling in this case, unless you are using walls. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Difficulty preparing a polymer (PEG) for simulation
On Mar 27, 2014 3:25 PM, Dan Sponseller grom...@danpeg.com wrote: I'm trying to prepare PEG for simulation in gromacs and running into considerable difficulties. My PEG chain is HOC-COC-COC..COC-COC-COH with appropriate hydrogens on the carbons. I am using the new CHARM36.ff Following the procedure for polymers, I added a beginning, and end, and a central chain piece to 'merged.rtp' and modified the atom names in the .pdb file to match. I have also added the residues to the 'residuetypes.dat' as Non-Protein (I have also tried listing it as a Protein). pdb2gmx claims I have169 missing atoms but will create the .gro and .top files anyway with the -missing parameter passed. The .gro file has all the atoms but the .top seems to be missing much information on bonds and angles. Probably no point in continuing but after a quick editconfig, grompp gives me a fatal error: Group Protein referenced in the .mdp file was not found in the index file. Well that one is easy - refer in the .mdp to the thing that is there, not what is not! I am new to gromacs and would really appreciate help getting started on its use like this. Following is some of my data files. Daniel Sponseller PhD student Computational Science and Informatics George Mason University Snip from 'merged.rtp' ;Dan Sponseller ;Copying from DME below for the repeating chain for PEG. [ LIG ] [ atoms ] C1 CC32A -0.010 0 H11 HCA2A0.090 1 H12 HCA2A0.090 2 OO2 OC30A -0.340 3 C3 CC32A -0.010 4 H31 HCA2A0.090 5 H32 HCA2A0.090 6 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define begining of chain for PEG. CH2-OH from [ ETOH ] [ LIGb ] [ atoms ] OO1 OG311 -0.650 0 H11 HGP10.420 1 C3 CG3210.050 2 H31 HGA20.090 3 H32 HGA20.090 4 [ bonds ] OO1 H11 OO1C3 C3 H31 C3 H32 C3 +C1 ;Dan Sponseller ;Next, define ending of chain for PEG. CH2-OH from [ ETOH ] [ LIGe ] [ atoms ] C1 CG3210.050 0 H11 HGA20.090 1 H12 HGA20.090 2 OO2 OG311 -0.650 3 H21 HGP10.420 4 [ bonds ] C1 -C3 C1 H11 C1 H12 C1 OO2 OO2 H21 Those files above seem fine, but pdb2gmx will have a hard time unscrambling your input .pdb file, which lists the atoms of end residue at the beginning and end, the beginning residue at the end, and interleaves residue numbering throughout. Those are probably not all deal breakers, but their combination is! An orderly progression from beginning to end is expected. Mark my modified 'PEG.pdb' file: COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL HETATM1 C1 LIGe1 -14.784 -1.665 0.506 1.00 0.00 C HETATM2 C3 LIG 2 -13.927 -1.410 -0.735 1.00 0.00 C HETATM3 OO2 LIG 2 -13.056 -0.302 -0.493 1.00 0.00 O HETATM4 H11 LIGe1 -15.383 -2.563 0.355 1.00 0.00 H HETATM5 H12 LIGe1 -14.137 -1.802 1.372 1.00 0.00 H HETATM6 H31 LIG 2 -13.333 -2.297 -0.956 1.00 0.00 H HETATM7 H32 LIG 2 -14.573 -1.185 -1.584 1.00 0.00 H HETATM8 C1 LIG 2 -12.207 0.022 -1.596 1.00 0.00 C HETATM9 C3 LIG 3 -11.325 1.216 -1.227 1.00 0.00 C HETATM 10 OO2 LIG 3 -10.441 0.845 -0.167 1.00 0.00 O HETATM 11 H12 LIG 2 -11.578 -0.836 -1.835 1.00 0.00 H HETATM 12 H11 LIG 2 -12.818 0.276 -2.463 1.00 0.00 H HETATM 13 H31 LIG 3 -10.741 1.519 -2.096 1.00 0.00 H HETATM 14 H32 LIG 3 -11.953 2.046 -0.903 1.00 0.00 H HETATM 15 C1 LIG 3 -9.568 1.894 0.257 1.00 0.00 C HETATM 16 C3 LIG 4 -8.673 1.387 1.389 1.00 0.00 C HETATM 17 OO2 LIG 4 -7.815 0.358 0.894 1.00 0.00 O HETATM 18 H11 LIG 3 -8.949 2.211 -0.582 1.00 0.00 H HETATM 19 H12 LIG 3 -10.160 2.738 0.611 1.00 0.00 H HETATM 20 H31 LIG 4 -8.070 2.210 1.772 1.00 0.00 H HETATM 21 H32 LIG 4 -9.294 0.988 2.192 1.00 0.00 H HETATM 22 C1 LIG 4 -6.933 -0.187 1.877 1.00 0.00 C HETATM 23 C3 LIG 5 -6.066 -1.274 1.239 1.00 0.00 C HETATM 24 OO2 LIG 5 -5.215 -0.687 0.252 1.00 0.00 O HETATM 25 H11 LIG 4 -6.294 0.603 2.270 1.00 0.00 H HETATM 26 H12 LIG 4 -7.517
Re: [gmx-users] Effect of a single mutation in a protein
On 3/27/14, 2:32 PM, Pappu Kumar wrote:
Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
atoms of one trajectory and then projected the other trajectory on it.
Sounds reasonable.
I obtained the ATP parameters from a paper. Like all simulations, MD has some
limitations. So I don't want to highlight the things which may not be correct.
OK, I thought you were trying to indicate something else. Presumably the ATP
parameters are pretty good; it's a standard molecule in just about every force
field.
There is no unfolding. Also the gibbs energy surface projected on PC1 and PC2
looks quite different than RMSD vs. Rg surface calculated by g_sham (also the
lowest energy structures.)
Without significant conformational changes, I still don't see how RMSD or Rg are
relevant metrics for what you're seeing.
Can I calculate del del G by TI? I am not sure how to define the reaction
coordinates. Is it a good idea to do umbrella sampling between two states to
determine the free energy?
The ddG of what? Folding? Ligand binding? Umbrella sampling isn't the best
approach here, but doing an alchemical transformation between the WT and mutant
might be possible. You'll have to define very clearly what you're trying to
achieve.
-Justin
On Thursday, 27 March 2014 8:35 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/26/14, 2:24 PM, Pappu Kumar wrote:
I have already used g_hbond. I am not sure how accurate is the H-bond
lifetime calculation. Also the trajectory snapshots need to be saved quite
often. Could you tell me how to interpret output from g_hbond -ac :
There should be references provided in the g_hbond output when calculating
lifetimes. At the very least, they're in the manual. So you can determine for
yourself how reliable the outcome is.
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
Plotting these data sets in XmGrace will clear things up.
Could you tell me how to project the configurations of the mutant simulation
on WT PC1? Are you aware of any paper where I can read more about it? Can I
compare the PC1 vs PC2 in case of WT and mutant?
See g_anaeig -h, as well as previous discussions in the list archive on doing
this.
I am trying to find out how such mutation buried inside the protein away from
the ligand binding pocket can influence the function of the protein. I actually
see some changes in the positon of the bound ATP in the mutant compared to the
WT. But I am not sure how reliable it is due to the inaccuracies in
parameterization.
Well, if your parametrization is inaccurate and you know it is, what use are the
simulations? Or are you just wondering if there is a possibility of
inaccuracies? Either way, that's something that should be sorted out long
before doing any real simulations :)
I also calculated the Gibbs free energy landscape by g_sham using Rg and
RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with ~0
kJ/mol has changed.
Do the proteins unfold? If not, I doubt Rg vs. RMSD is a very sensitive metric
of anything. You can, of course, map back the locations of the energy minima to
see if there are any interesting differences there, but such a plot (Rg vs.
RMSD) is probably only useful in protein (un)folding simulations.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu mailto:jalem...@outerbanks.umaryland.edu |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
Gromacs Users mailing list
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