[gmx-users] g_hbond (Version 3.3 vs Version 3.14)
Anil Kumar
anil at chem.iitb.ac.in
Thu Dec 20 02:18:50 CET 2007
Dear All,
I found there is some problem with version 3.3 to g_hbond command. Earlier
i was using version 3.14, and when i was using g_hbond(v3.14) i found
correct distribution of hydrogen bond pattern (i.e., n-n+1,n-n+2, n-n+3 so
on).
But when i use g_hbond (v3.3) then i found it only gives hydrogen bonds
between n-n, n-n+1,n-n+2 and rest will have value zero.
Is it some bug to version 3.3 or am i doing mistake !
thanks in advance.
Regards,
anil
--
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ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Mumbai-400076,
Ph. No.-022-25764780(Lab)
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Mumbai-400076,Ph.No.:-+91-9819638547 (Mobile)
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> Today's Topics:
>
> 1. Re: membranes & proteins revisited (Alan Dodd)
> 2. Re: HELP REGARDING COMMAND g_pvd (Jochen Hub)
> 3. Re: Membrane protein simulation (Yanzi Zhou)
> 4. regarding range checking error and constraint errors in Lincs
> algorithm (shyamala iyer)
> 5. Re: regarding range checking error and constraint errors in
> Lincs algorithm (Matt Wyczalkowski)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 Dec 2007 04:58:16 -0800 (PST)
> From: Alan Dodd <anoddlad at yahoo.com>
> Subject: Re: [gmx-users] membranes & proteins revisited
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <714114.80284.qm at web38711.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Of course it's unnatural, it's a membrane made of gas instead of lipid ;)
> I'd recommend that you equilibrate the "membrane" first, and check it
> actually behaves in a manner close enough to one for what you want - and
> then insert a protein into it. You might want to look into the make_hole
> suite on the user contributions page, it's designed to make a hole in a
> lipid membrane for a protein, but I'm sure modifying it for argon would be
> rather trivial.
>
> ----- Original Message ----
> From: Magnus Andersson <magnus.andersson at chalmers.se>
> To: gmx-users at gromacs.org
> Sent: Tuesday, December 18, 2007 9:38:09 PM
> Subject: [gmx-users] membranes & proteins revisited
>
> Hi all,
>
> I have a trimer membrane protein structure & an artificial Argon grid
> membrane (100x100x30Å).
>
> First I wonder whether you should equilibrate the membrane first (it looks
> very un-natural, like a perfect grid...) and then physically remove atoms
> where I want to have my protein, then run:
> genbox -cp protein.gro -cs membrane.gro
>
> if I just run it as it is, I get:
>
> Checking Protein-Solvent overlap: tested 1512 pairs, removed 9261 atoms.
>
> I feel I'm getting there, but need some advice to come to the point where
> I have my trimer in a "relaxed" membrane...
>
> Thanks /
>
> Magnus
> --
> Magnus Andersson
>
> Chalmers University of Technology
> Dept of Chemistry and Biological Engineering
> Email: magnus.andersson at chalmers.se
> Homepage: http://www.csb.gu.se/neutze/
> Phone: +46 (0)31-786 3917
> Fax: +46 (0)31-786 3910
> Lundberg Laboratory
> Medicinaregatan 9e
> SE-413 90 Göteborg
> Sweden
>
> _______________________________________________
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 19 Dec 2007 15:10:41 +0100
> From: Jochen Hub <jhub at gwdg.de>
> Subject: Re: [gmx-users] HELP REGARDING COMMAND g_pvd
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47692661.8040905 at gwdg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> avinash kumar wrote:
>> Hello all,
>> I saw a command in the analysis part of manual in section 8.14
>> . The command name is g_pvd . It says it can calculate properties like
>> density of particles per unit volume but I donot find it in the manual
>> nor in my GROMACS installation. Can anybody help me on this?
>>
> Check g_density.
>
>>
>> Avinash Kumar
>> Mechanical engineering
>> IIT Kharagpur
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>> .
>>
>>
>
>
> --
> ************************************************
> Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> ************************************************
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 19 Dec 2007 13:10:23 -0500
> From: Yanzi Zhou <yz30 at nyu.edu>
> Subject: Re: [gmx-users] Membrane protein simulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47695E8F.1050804 at nyu.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Dear Behnoush:
>> Dear Yanzi,
>> Forthunatly my simulation was run. this time I select the pope files of
>> the Dr Tieleman's site and create the protein_in_pope.pdb with ffgmx
>> force field.
>> Then I ran genbox to solvate the system and delete some pope which had
>> crash with the protein.Also I added #include "lipid.itp" in the last
>> generated .top file and change the charactr of system at the end of the
>> file based on the total number of protein.pope and water. So grompp has
>> been run.
>> But I have already two questions. After grompp, I ran genion to
>> neutralize the system. But this run has not any output and it seems it
>> has stopped in this step by these two lines in the end:
>>
>> Number of (3-atomic) solvent molecules: 6113
>> Replacing solvent molecule 717 (atom 18791) with CL-
>>
>>
> It means that the system has 6113 solvent molecules and one of them is
> replaced by CL-. So you can find the coordinate file named out.gro, and
> if you have used the option "-p topol.top", you will find your topolopy
> file has changed also.
>> and there is no interaction. Could you please explain to me what it
>> means and what I should do.
>> Another problem is the protein size is greater than the box in the both
>> sides. What is your suggestion to me for expanding the water size in
>> both sides of the box?
> What do you mean by both sides? If you mean the Z axis, you should
> expand the box and add more water, because we use period boundary
> conditions, the protein doesn't want to see itself. But be careful, POPE
> may not suitable for this protein. If you mean the X or Y axis, you
> should use a larger system of POPE, more lipids and more water.
>> Thank you very much in advance for your very kind help.
>>
>> Best regards
>> Behnoush
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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
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>>
>>
> Best Regards.
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 19 Dec 2007 12:57:09 -0800
> From: "shyamala iyer" <shyamala.iyer at gmail.com>
> Subject: [gmx-users] regarding range checking error and constraint
> errors in Lincs algorithm
> To: gmx-users at gromacs.org
> Message-ID:
> <d57256d60712191257w1581d240l51e277c5a46ca2fb at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi gromacs users,
>
> I apologize in advance for the long mail, but I have been having some
> trouble with my gromacs simulations lately.
>
> My system consists of two popypeptide chains and a small ligand (or
> drug like compound). I obtain the required gromacs topologies for the
> ligand/drug from PRODRG dundee server. The steps I use for a MD
> simulation using gromacs is briefly as follows:
> 1) get ligand file with required polar hydrogens and gromacs ligand
> .itp file from prodrg server
> 2) run pdb2gmx using the gmx force field and spce water
> 3) correctly update the protein topology file to include ligand itp
> file header, number of ligand molecules and also make sure the output
> file from pdb2gmx contains the necessary ligand coordinates
> 3) set up box around this system, fill box with solvent (water),
> neutralize system using genion
> 4) set up files to run energy minimization on system, run energy
> minimization
> 5) set up files to run position restrained dynamics and run position
> restrained dynamics
> 6) setup up files and run Molecular dynamics on the system for ~ 10 ps
> The above set up worked with one of the protease-ligand complex I was
> testing, but had been failing for another viral protease.
>
> The errors vary depending on the run, and in some simulations, I get
> an error during the Energy minimization step: (section of em log file
> pasted below)
> ------------------------------------------------------------
>
>
> Enabling SPC water optimization for 41607 molecules.
>
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G.
> Pedersen
>
> A smooth particle mesh Ewald method
>
> J. Chem. Phys. 103 (1995) pp. 8577-8592
>
> -------- -------- --- Thank You --- -------- --------
>
> Removing pbc first time
>
> Done rmpbc
>
> 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: 129215
>
> Started Steepest Descents on node 0 Wed Dec 19 10:33:25 2007
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>
> S. Miyamoto and P. A. Kollman
>
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for
> Rigid Water Models
>
> J. Comp. Chem. 13 (1992) pp. 952-962
>
> -------- -------- --- Thank You --- -------- --------
>
> Steepest Descents:
>
> Tolerance (Fmax) = 1.00000e+02
>
> Number of steps = 100
>
> Going to use C-settle (41607 waters)
>
> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
>
> rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
>
> Grid: 15 x 15 x 15 cells
>
> Configuring nonbonded kernels...
>
> Testing x86_64 SSE support... present.
>
> Step Time Lambda
>
> 0 0.00000 0.00000
>
> -------------------------------------------------------
>
> Program mdrun, VERSION 3.3.1
>
> 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.
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 3375
> ]
>
> Please report this to the mailing list (gmx-users at gromacs.org)
>
> -------------------------------------------------------
>
> At the end of this mail I have also pasted the em.mdp file I use to
> set up energy minimizations. I would really appreciate it if someone
> could help me address this Range checking error issue.
>
> Another type of error that I recently encountered occurs during
> position restrained dynamics simulations. The error is a constraint
> error in Lincs algorithm at a particular time step and usually is
> accompanied by a line that is similar to, (with time and atom number
> varying )
> -----------------------------------------------------------------------------------------------------------------------------------------
> t= 0.02ps Water molecule starting at atom 71500 can not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
> previous and current coordinates
> -------------------------------------------------------------------------------------------------------------------------------------------
> I have triend reducing the time step and I still get the same error.
> I have also pasted the pr.mdp file I use to set up and run position
> restrained dynamics.
> I would like some help in solving this lincs error issue.
>
> The original protease pdb file that I used for the above simulations
> has a small segment missing from chain A. This loop segment was highly
> disorderd in the cystal structure hence, coordinates for this 7
> residue segment is missing in the pdb file. This missing segment is no
> where near where the ligand is bound on the protease. Does a missing
> segment cause problems during siumlations?
>
> Another general question on the genion function:
> Is there a way I could not have genion be interactive. My systems
> usually have a protein, a ligand and water, and I always choose group
> 13 (SOL) as the selection after running genion. I am asking this
> because there are times when I want to run the same protein with
> several different ligands and I would like a script to run through all
> gromacs steps and not have a particular step be interactive.
>
>
> Thanks for reading a long mail.
> Shyamala
> ------------------------------------------------------
> em.mdp
> title = fws
> cpp = /usr/bin/cpp ; location of cpp
> define = -DFLEX_SPC
> constraints = none
> integrator = steep
> dt = 0.001 ; ps !
> nsteps = 100 ; 100 steps of energy min
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> table-extension = 3.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ;
> ; Energy minimizing stuff
> ;
> emtol = 100.0
> emstep = 0.01
> -------------------------------------------------------
> pr.mdp
> title = fws
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 10.0 ps.
> nstcomm = 1
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc_grps = protein non-protein
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 19 Dec 2007 15:10:29 -0600
> From: Matt Wyczalkowski <maw2 at cec.wustl.edu>
> Subject: Re: [gmx-users] regarding range checking error and constraint
> errors in Lincs algorithm
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <476988C5.9010007 at cec.wustl.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Funny enough, I came across the same problem just earlier today, with
> the same large, negative ci value.
>
> Setting the constraints as follows seemed to fix the problem,
>
> constraints = all-bonds
>
> Good luck,
>
> Matt
>
> shyamala iyer wrote:
>> Hi gromacs users,
>>
>> I apologize in advance for the long mail, but I have been having some
>> trouble with my gromacs simulations lately.
>>
>> My system consists of two popypeptide chains and a small ligand (or
>> drug like compound). I obtain the required gromacs topologies for the
>> ligand/drug from PRODRG dundee server. The steps I use for a MD
>> simulation using gromacs is briefly as follows:
>> 1) get ligand file with required polar hydrogens and gromacs ligand
>> .itp file from prodrg server
>> 2) run pdb2gmx using the gmx force field and spce water
>> 3) correctly update the protein topology file to include ligand itp
>> file header, number of ligand molecules and also make sure the output
>> file from pdb2gmx contains the necessary ligand coordinates
>> 3) set up box around this system, fill box with solvent (water),
>> neutralize system using genion
>> 4) set up files to run energy minimization on system, run energy
>> minimization
>> 5) set up files to run position restrained dynamics and run position
>> restrained dynamics
>> 6) setup up files and run Molecular dynamics on the system for ~ 10 ps
>> The above set up worked with one of the protease-ligand complex I was
>> testing, but had been failing for another viral protease.
>>
>> The errors vary depending on the run, and in some simulations, I get
>> an error during the Energy minimization step: (section of em log file
>> pasted below)
>> ------------------------------------------------------------
>>
>>
>> Enabling SPC water optimization for 41607 molecules.
>>
>> Will do PME sum in reciprocal space.
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>
>> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G.
>> Pedersen
>>
>> A smooth particle mesh Ewald method
>>
>> J. Chem. Phys. 103 (1995) pp. 8577-8592
>>
>> -------- -------- --- Thank You --- -------- --------
>>
>> Removing pbc first time
>>
>> Done rmpbc
>>
>> 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: 129215
>>
>> Started Steepest Descents on node 0 Wed Dec 19 10:33:25 2007
>>
>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>
>> S. Miyamoto and P. A. Kollman
>>
>> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for
>> Rigid Water Models
>>
>> J. Comp. Chem. 13 (1992) pp. 952-962
>>
>> -------- -------- --- Thank You --- -------- --------
>>
>> Steepest Descents:
>>
>> Tolerance (Fmax) = 1.00000e+02
>>
>> Number of steps = 100
>>
>> Going to use C-settle (41607 waters)
>>
>> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
>>
>> rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
>>
>> Grid: 15 x 15 x 15 cells
>>
>> Configuring nonbonded kernels...
>>
>> Testing x86_64 SSE support... present.
>>
>> Step Time Lambda
>>
>> 0 0.00000 0.00000
>>
>> -------------------------------------------------------
>>
>> Program mdrun, VERSION 3.3.1
>>
>> 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.
>>
>> Variable ci has value -2147483648. It should have been within [ 0 ..
>> 3375 ]
>>
>> Please report this to the mailing list (gmx-users at gromacs.org)
>>
>> -------------------------------------------------------
>>
>> At the end of this mail I have also pasted the em.mdp file I use to
>> set up energy minimizations. I would really appreciate it if someone
>> could help me address this Range checking error issue.
>>
>> Another type of error that I recently encountered occurs during
>> position restrained dynamics simulations. The error is a constraint
>> error in Lincs algorithm at a particular time step and usually is
>> accompanied by a line that is similar to, (with time and atom number
>> varying )
>> -----------------------------------------------------------------------------------------------------------------------------------------
>> t= 0.02ps Water molecule starting at atom 71500 can not be settled.
>> Check for bad contacts and/or reduce the timestep.Wrote pdb files with
>> previous and current coordinates
>> -------------------------------------------------------------------------------------------------------------------------------------------
>> I have triend reducing the time step and I still get the same error.
>> I have also pasted the pr.mdp file I use to set up and run position
>> restrained dynamics.
>> I would like some help in solving this lincs error issue.
>>
>> The original protease pdb file that I used for the above simulations
>> has a small segment missing from chain A. This loop segment was highly
>> disorderd in the cystal structure hence, coordinates for this 7
>> residue segment is missing in the pdb file. This missing segment is no
>> where near where the ligand is bound on the protease. Does a missing
>> segment cause problems during siumlations?
>>
>> Another general question on the genion function:
>> Is there a way I could not have genion be interactive. My systems
>> usually have a protein, a ligand and water, and I always choose group
>> 13 (SOL) as the selection after running genion. I am asking this
>> because there are times when I want to run the same protein with
>> several different ligands and I would like a script to run through all
>> gromacs steps and not have a particular step be interactive.
>>
>>
>> Thanks for reading a long mail.
>> Shyamala
>> ------------------------------------------------------
>> em.mdp
>> title = fws
>> cpp = /usr/bin/cpp ; location of cpp
>> define = -DFLEX_SPC
>> constraints = none
>> integrator = steep
>> dt = 0.001 ; ps !
>> nsteps = 100 ; 100 steps of energy min
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdwtype = cut-off
>> rvdw = 1.4
>> table-extension = 3.0
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 6
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 100.0
>> emstep = 0.01
>> -------------------------------------------------------
>> pr.mdp
>> title = fws
>> cpp = /usr/bin/cpp
>> define = -DPOSRES
>> constraints = all-bonds
>> integrator = md
>> dt = 0.002 ; ps !
>> nsteps = 5000 ; total 10.0 ps.
>> nstcomm = 1
>> nstxout = 250
>> nstvout = 1000
>> nstfout = 0
>> nstlog = 10
>> nstenergy = 10
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdwtype = cut-off
>> rvdw = 1.4
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 6
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ; Berendsen temperature coupling is on
>> Tcoupl = berendsen
>> tau_t = 0.1 0.1
>> tc_grps = protein non-protein
>> ref_t = 300 300
>> ; Pressure coupling is on
>> Pcoupl = berendsen
>> pcoupltype = isotropic
>> tau_p = 1.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = 173529
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>
>
> --
> Matt Wyczalkowski
> Doctoral Candidate, Biomedical Engineering
> Pappu Lab: http://lima.wustl.edu
> Washington University in St. Louis
> maw2 at cec.wustl.edu
>
>
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 44, Issue 60
> *****************************************
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