[gmx-users] indexing largest cluster with g_clustsize
Dear gmx'ers! One more question on g_clustsize routine: It produces an index file with the atom numbers of largest cluster. But how it works in an evaporating system where the number of clustered molecules reduces greatly through the trajectory? What frame the maxclust.ndx file concerns to? -- Regards Dmitri mailto:ddu...@ngs.ru___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] number of coordinates in coordinate file does not match topology
Dear ALL, I am running simulation for the drug enzyme complex using Gromacs with gromacs96(43a2)forcefield. After generating waterbox around my protein, when I am running grompp command (before energy minimization) I am getting following error: --- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 735 Excluding 3 bonded neighbours for ZPR 1 Excluding 2 bonded neighbours for SOL 36755 NOTE: System has non-zero total charge: -1.99e+01 processing coordinates... -- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (protein_gen.pdb, 119825) does not match topology (topology.top, 119830) -- I checked gromacs wiki page also(http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology) but not able to solve this error.I am getting this error before adding ions. Can anybody help me regarding same and suggest what could be possible reason for this ? Thanks, Regards, -- Swati kaushik Research Scholar Prof. R. Sowdhamini's lab National Center for Biological Sciences Tata Institute of Fundamental Research UAS-GKVK campus Bellary road, Bangalore- 560065 India Phone: Lab: 0(91)80- 23 66 62 51 0(91)80- 67 17 62 51 Fax: 0(91) 80 23 63 66 62 Email: swa...@ncbs.res.in swati.kaushi...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] indexing largest cluster with g_clustsize
Hi Dmitri, It's the last frame - the file is written after all frames are read and dealt with. Best regards, Ran Dmitri Dubov wrote: Dear gmx'ers! One more question on g_clustsize routine: It produces an index file with the atom numbers of largest cluster. But how it works in an evaporating system where the number of clustered molecules reduces greatly through the trajectory? What frame the maxclust.ndx file concerns to? -- Regards Dmitri mailto:ddu...@ngs.ru ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] charge from propene?
Dear all, I have a problem with a propene molecule: does anybody know what the best charge for the propene atoms is? Thank you for your efforts. Saskia Frenzel -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: number of coordinates in coordinate file does not match topology
I am running simulation for the drug enzyme complex using Gromacs with gromacs96(43a2)forcefield. After generating waterbox around my protein, when I am running grompp command (before energy minimization) I am getting following error: --- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 735 Excluding 3 bonded neighbours for ZPR 1 Excluding 2 bonded neighbours for SOL 36755 NOTE: System has non-zero total charge: -1.99e+01 processing coordinates... -- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (protein_gen.pdb, 119825) does not match topology (topology.top, 119830) -- I checked gromacs wiki page also( http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology ) but not able to solve this error.I am getting this error before adding ions. Can anybody help me regarding same and suggest what could be possible reason for this ? Thanks, Regards, I guess you just missed five atoms in your gro file. Does the number of solvent molecules in the coordinate file equal to that in the topology? ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: number of coordinates in coordinate file does not match topology
It seems atoms, not molecules... :) ~Vitaly On Thu, Jul 16, 2009 at 12:36 PM, swa...@ncbs.res.in wrote: Hi, thanks for your reply. Yes their is difference of 5 solvent molecules. They are more in number in my topology file. Regards, Swati I am running simulation for the drug enzyme complex using Gromacs with gromacs96(43a2)forcefield. After generating waterbox around my protein, when I am running grompp command (before energy minimization) I am getting following error: --- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 735 Excluding 3 bonded neighbours for ZPR 1 Excluding 2 bonded neighbours for SOL 36755 NOTE: System has non-zero total charge: -1.99e+01 processing coordinates... -- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (protein_gen.pdb, 119825) does not match topology (topology.top, 119830) -- I checked gromacs wiki page also( http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology ) but not able to solve this error.I am getting this error before adding ions. Can anybody help me regarding same and suggest what could be possible reason for this ? Thanks, Regards, I guess you just missed five atoms in your gro file. Does the number of solvent molecules in the coordinate file equal to that in the topology? ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] How does pdb2gmx assign protonation in default condition?
Liu Ji wrote: Hi all, I have a question about how pdb2gmx determines the protonation of the His residue in default. To best of my knowledge, His usually has its ND1 nitrogen free in un-protonated state, which might equal to the HISB presents in pdb2gmx. However, when I am treating pdb files by pdb2gmx without specifing exact state of His, the resulting structure contains both HISA (NE2 free) and HISB (ND1 free) state as something listed below, There are 1155 hydrogen bonds Will use HISB for residue 151 Will use HISB for residue 218 Will use HISB for residue 368 Will use HISA for residue 425 Will use HISB for residue 449 I am assuming that the hydrogen has been added in consideration of steric interaction, however, does this assignment violate the common knowledge? I can't find any references about this issue and am not sure how large influence will be generated. So can you give me any suggestions? Thanks a lot. Quoting from pdb2gmx -h: ...for HIS the proton can be either on ND1 (HISA), on NE2 (HISB) or on both (HISH). By default these selections are done automatically. For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively. -Justin Liu Ji Institute of Bioengineering Zhejiang University, China ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Segmentation Fault (Address not mapped)
darre...@ece.ubc.ca wrote: Hi Mark, I do not do any equilibration, I only do energy minimization as in the GROMACS Tutorial for Solvation Study of Spider Toxin Peptide. Please let me know if I need to do equilibration and what is the difference between energy minimization and equilibration as this is not clear to me. Did the EM converge satisfactorily? What was Fmax? Unlike EM, equilibration is an MD process; for a protein system, one generally position-restrains the protein and allows the surrounding solvent to optimize around the structure. -Justin Here is an mdp file for a run that actually completed successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =1 nstcomm =100 nstxout =100 ;nstvout=1000 nstfout =0 nstlog =100 nstenergy =100 nstlist =100 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 And here is a copy of an mdp file for a run that did not complete successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =3 nstcomm =500 nstxout =500 ;nstvout=1000 nstfout =0 nstlog =500 nstenergy =500 nstlist =500 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Please let me know what you think might be the problem. Thanks Darrell Date: Thu, 16 Jul 2009 09:47:49 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5e6aa5.4040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, Yes, I know that the box dimensions are defined in the last line of the .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm in the .gro file. OK. I looked through my .gro file to ensure none of the atoms had coordinates outside the 38x38x38 box. While I was reviewing the file I did notice that some coordinates had negative values, slightly negative, but negative none the less. Could this be causing the segmentation fault between time step 10,000 and time step 30,000? Why wouldn't the negative coordinates cause a segmentation fault much earlier? The absolute value of the coordinates is irrelevant. Your choice of 2.0 for rcoulomb is likely suboptimal for PME. Some smaller value is probably more efficient, but this will not be the cause of your problem. What is your system preparation regime? (i.e. EM + equilibration) Can you post a corrected and current .mdp file? Mark Date: Wed, 15 Jul 2009 16:59:21 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5d7e49.9020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Justin, I was experiencing the problem before someone suggested using editconf so I do not think the problem is being caused by editconf. But anyway here is my editconf command. Let me know if you a source of error in this command line. editconf -f graphene.gro -n index.ndx -o graphene_ec.gro I did not want to add in additional space between the solvent and the box as I saw no reason for doing so. And hence that is why I originally did not use editconf. My box
Re: [gmx-users] charge from propene?
Saskia Frenzel wrote: Dear all, I have a problem with a propene molecule: does anybody know what the best charge for the propene atoms is? That depends entirely upon the force field you are trying to use. See, for example: http://oldwiki.gromacs.org/index.php/Parameterization -Justin Thank you for your efforts. Saskia Frenzel -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: number of coordinates in coordinate file does not match topology
By hand is the easiest way. Ya, sorry I wrote it wrong.But why these extra atoms are present in my topology file and how to correct it. Thanks, Regards, Swati On Thu, Jul 16, 2009 at 12:36 PM, swa...@ncbs.res.in wrote: Hi, thanks for your reply. Yes their is difference of 5 solvent molecules. They are more in number in my topology file. Regards, Swati I am running simulation for the drug enzyme complex using Gromacs with gromacs96(43a2)forcefield. After generating waterbox around my protein, when I am running grompp command (before energy minimization) I am getting following error: --- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 380 of the 1326 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 735 Excluding 3 bonded neighbours for ZPR 1 Excluding 2 bonded neighbours for SOL 36755 NOTE: System has non-zero total charge: -1.99e+01 processing coordinates... -- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (protein_gen.pdb, 119825) does not match topology (topology.top, 119830) -- I checked gromacs wiki page also( http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology ) but not able to solve this error.I am getting this error before adding ions. Can anybody help me regarding same and suggest what could be possible reason for this ? Thanks, Regards, I guess you just missed five atoms in your gro file. Does the number of solvent molecules in the coordinate file equal to that in the topology? ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] coarse-grained simulation of proteins
Hi, everyone. I'm trying a coarse-grained simulation with three beads representing the backbone structure of each residue. However, it's difficult to get the LJ parameters for -NH- and -CO- . Could anyone possibly know some work on this? Thanks in advance. Cristty ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] coarse-grained simulation of proteins
I'm trying a coarse-grained simulation with three beads representing the backbone structure of each residue. However, it's difficult to get the LJ parameters for -NH- and -CO- . Could anyone possibly know some work on this? Well, there is no magic parameters for NH or CO for a Coarse-grain simulation! These would be effective interaction and therefore depend entirely of the rest of the interaction you are using! You'll have to parameterize them to reproduce data that you think relevant. It is a very vague answer, sorry, but your question suggests that you should try some literature on the subject force field parameterization and coarse-graining. hope this helps. XAvier. Thanks in advance. Cristty ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 mailing listgmx-users@gromacs.org http://lists.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
RE: [gmx-users] making a box of water
Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Will #include ffgmx.itp solve my problem? Would it be a general solution or in each case I should specify (if I add other solutes such as proteins)? Well, ffgmx is deprecated, so it is probably not the best choice :) Choosing a force field should not be a haphazard occasion, it is a very important choice. For water models, parameters should be uniform, but if you're simulating a protein, you'll want to make a very educated decision. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:07 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water You need to #include an appropriate force field that contains the [defaults], [atomtypes], etc. before you can define a [moleculetype]. -Justin Payman Pirzadeh wrote: Here is my .top file: ;This includes SPC-E potential #include spce.itp [ system ] Pure box of water [ molecules ] SOL 515 I used the same
Re: [gmx-users] Hydroxide Ion
Hi, Well, it's not just a matter of topology. This is only true if the basic assumption holds, that the particles behave approximately classical. This is definitely not the case for species such as hydroxide and hydronium. Cheers, Tsjerk On Thu, Jul 16, 2009 at 4:13 AM, Justin A. Lemkuljalem...@vt.edu wrote: Marc Charendoff wrote: Hello, I am needing to include a single hydroxide ion in my simulation - is there a force field available in Gromacs that is already parameterized, or do I need to create from scratch? With regards to topology, same question, especially as PRODRG does not do mono or diatomics. Any guidance anyone could provide would be very much appreciated. I have tried searching the archives but didn't find anything. No, you'll need to do it yourself. The topology should be trivial - two atoms, one bond. As for what parameters to assign, there you've got your work cut out for you. -Justin Thanks Marc Charendoff ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] making a box of water
Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Will #include ffgmx.itp solve my problem? Would it be a general solution or in each case I should specify (if I add other solutes such as proteins)? Well, ffgmx is deprecated, so it is probably not the best choice :) Choosing a force field should not be a haphazard occasion, it is a very important choice. For water models, parameters should be uniform, but if you're simulating a protein, you'll want to make a very educated decision. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:07 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water You need to #include an appropriate force field that contains the [defaults],
RE: [gmx-users] making a box of water
But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Will #include ffgmx.itp solve my problem? Would it be a general solution or in each case I should specify (if I add other solutes such as proteins)? Well, ffgmx is deprecated, so it is probably not the best choice :) Choosing a force field should not be a haphazard occasion, it is a very important choice. For water models,
Re: [gmx-users] making a box of water
Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Will #include ffgmx.itp solve my problem? Would it be a general
Re: [gmx-users] making a box of water
Justin A. Lemkul wrote: Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. Works fine if the format is correct. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL 506 But I still get the same error message! Should I include the [defaults] in the .itp file? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 14, 2009 7:56 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman
RE: [gmx-users] making a box of water
You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:08 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairsFudgeLJ FudgeQQ N 1 2 NO ; include TIP4P topology #include tip4p.itp [ system ] Pure box of water [ molecules ] SOL
Re: [gmx-users] making a box of water
Payman Pirzadeh wrote: You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? As long as those vectors define the box size and not necessarily the system size (i.e., largest coordinate - smallest coordinate). You can do this with a .pdb file, I think on the CRYST line, if you prefer. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 12:08 PM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: But, I am using a .pdb file as the input of the gromacs. Does the preparation of pdb file differ from software to software? It shouldn't, and I'm not 100% sure on how Gromacs handles system size from a .pdb file (I always use .gro). What you can try to do is transform your .pdb into .gro format with editconf, and read the last line of the .gro file. That's any easy way to determine the size of the box Gromacs is finding. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 16, 2009 11:42 AM To: Gromacs Users' List Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the rvdw cutoff to 10A, but problem was still there. Now I made my box bigger by using a visualization software. The new dimensions are ~54*63*103.38(all in A). Again the same warning is given to me about increasing the box size or reduce the rvdw. Well, Gromacs doesn't do anything in A, it's all nm, so be sure that everything you're doing is consistent with Gromacs conventions. There is no reason that either of those boxe should be complaining about a 1.0-nm cutoff, so there has to be something that messed up along the way. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 7:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hello, I have an .pdb file from another simulation. I want to make the appropriate input files to run a simulations. I have used grompp to produce the .tpr file, but I get the usual ERROR: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rvdw. I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but still the problem persists! Smaller rvdw is not good for my system. Any suggestions? Then you'll have to use a bigger box, most likely. What is your smallest box vector? That should indicate the limits of your cutoffs. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: July 15, 2009 12:23 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Thanks Justin. Unfortunately, I realized that after I sent the e-mail. Anyways, I started running to models: SPCE and TIP4P to check the energies of these systems to figure out where the problem with my own system (six-site model) could be. I will keep you posted. But, I have a question about the compressibility factor used in .mdp file. Does that(if it is not a correct value) truly affect the simulation when the reference pressure is set? No, only the relaxation rate (with Berendsen scaling) resp. the oscillation period with Parrinello Rahman. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: July 15, 2009 11:38 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: Hi again, I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes in the [atoms ]are specifies as opls_???, doesn't grompp check the database for the corresponding parameters? Or we should again manually specify the [ atomtypes ] again in either .itp or .top file? You need to #include ffoplsaa.itp to take care of everything related to the OPLS-AA force field. Invoking grompp is not magic, the topology has to contain specific instructions for everything you need to handle in your system. -Justin Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Payman Pirzadeh Sent: July 15, 2009 10:14 AM To: jalem...@vt.edu; 'Discussion list for GROMACS users' Subject: RE: [gmx-users] making a box of water OK! I changed my .top file to ;This is simulation for TIP4P water model [ defaults ] ; non-bondedtypecombrulegenpairs
Re: [gmx-users] making a box of water
Payman Pirzadeh wrote: You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? Set them using editconf Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Forcefields and water models for protein simulations.
Dear All, I recently asked a question about comparing the forcefields for protein simulations and the appropriate water model to use for the same to which Justin answered back. Thanks for the answer justin. In addition, I found a couple of references which I think are really good for the above topics which I would like to share with other newbies (like me) as a future reference. This might be a good starting point for other to follow. They are: For the forcefields: 1: Methods Mol Biol. 2008;443:63-88. Links Comparison of protein force fields for molecular dynamics simulations. Guvench O, MacKerell AD Jr. Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA. In the context of molecular dynamics simulations of proteins, the term force field refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules. For the water models. 2: 1: J Chem Phys. 2005 Apr 1;122(13):134508. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. Shirts MR, Pande VS. Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA. Quantitative free energy computation involves both using a model that is sufficiently faithful to the experimental system under study (accuracy) and establishing statistically meaningful measures of the uncertainties resulting from finite sampling (precision). In order to examine the accuracy of a range of common water models used for protein simulation for their solute/solvent properties, we calculate the free energy of hydration of 15 amino acid side chain analogs derived from the OPLS-AA parameter set with the TIP3P, TIP4P, SPC, SPC/E, TIP3P-MOD, and TIP4P-Ew water models. We achieve a high degree of statistical precision in our simulations, obtaining uncertainties for the free energy of hydration of 0.02-0.06 kcal/mol, equivalent to that obtained in experimental hydration free energy measurements of the same molecules. We find that TIP3P-MOD, a model designed to give improved free energy of hydration for methane, gives uniformly the closest match to experiment; we also find that the ability to accurately model pure water properties does not necessarily predict ability to predict solute/solvent behavior. We also evaluate the free energies of a number of novel modifications of TIP3P designed as a proof of concept that it is possible to obtain much better solute/solvent free energetic behavior without substantially negatively affecting pure water properties. We decrease the average error to zero while reducing the root mean square error below that of any of the published water models, with measured liquid water properties remaining almost constant with respect to our perturbations. This demonstrates there is still both room for improvement within current fixed-charge biomolecular force fields and significant parameter flexibility to make these improvements. Recent research in computational efficiency of free energy methods allows us to perform simulations on a local cluster that previously required large scale distributed computing, performing four times as much computational work in approximately a tenth of the computer time as a similar study a year ago. Thanks Rama ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Peptide - DMPC membrane simulations - Unstable system
Hi guys, I am trying to start simulation on lipid - peptide system, but receive LINCS warnings of angles rotating more than 30 deg which means that my system is unstable. I have tried to do mdrun on the DMPC box itself and had no problems. Once I insert my peptide, the problems starts. I have run Energy MInimization with LIncs order or 4 and Lincs iterations 8, but still could not bring system to 200 kJ/mol Fmax. Received the following message. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2# Steepest Descents converged to machine precision in 499 steps, but did not reach the requested Fmax 100. Potential Energy = -1.2830664e+06 Maximum force = 3.4162991e+03 on atom 2 Norm of force = 3.2566280e+01 Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in water box just to see if it will work. My questions: -How to position peptide into existing lipid box (apart form using editconf -rotate parameter). I have tried VMD and did it visually, but new coordingates were not saved? -How I can improve on EM, what kinda setting in mdp file can I use to that system converges even after 10,000 steps? -How to prevent clashes, maybe there are some settings to try with genbox -cp -cs command? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system
Kirill Bessonov wrote: Hi guys, I am trying to start simulation on lipid - peptide system, but receive LINCS warnings of angles rotating more than 30 deg which means that my system is unstable. I have tried to do mdrun on the DMPC box itself and had no problems. Once I insert my peptide, the problems starts. I have run Energy MInimization with LIncs order or 4 and Lincs iterations 8, but still could not bring system to 200 kJ/mol Fmax. Received the following message. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2# Steepest Descents converged to machine precision in 499 steps, but did not reach the requested Fmax 100. Potential Energy = -1.2830664e+06 Maximum force = 3.4162991e+03 on atom 2 Norm of force = 3.2566280e+01 Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in water box just to see if it will work. My questions: -How to position peptide into existing lipid box (apart form using editconf -rotate parameter). I have tried VMD and did it visually, but new coordingates were not saved? I wrote a tutorial that gives instructions on how to build membrane protein systems, you might find it useful: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -How I can improve on EM, what kinda setting in mdp file can I use to that system converges even after 10,000 steps? emstep and emtol are the relevant parameters. Setting nsteps is the maximum amount of steps allowed; I don't think there is a way (or a reason) to force EM to run to 10,000 steps. -How to prevent clashes, maybe there are some settings to try with genbox -cp -cs command? You could use genbox, but often what happens is there are substantial voids between the peptide and lipids. Water seeps in and you have to equilibrate for a lot longer. See my tutorial above for more rigorous building methods. -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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: Extend water layer along negative Z-direction
You can try to position your system in Z direction using: editconf -princ (and bunch of other normal parameters) Also you can use -rotate parameter to align your system along any axis Hope it helps ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Segmentation Fault (Address not mapped)
Hi Justin, Thanks for the explanation of the difference between EM equilibration. Since in my model, I: (i) only have the graphene sheet and ammonia molecules spaced reasonably far apart from each other (1332 NH3 molecules in a 38x38x38 box) and from the graphene sheet (distance between the closest ammonia molecule and the graphene sheet is greater than the molecular diameter of ammonia - maybe this is too close and could be causing my problem?); (ii) freeze the graphene sheet; I am thinking equilibration is not required in my model. Please let me know if you think I still need to perform equilibration. Yes, the EM did converge satisfactorily. Here is the output from EM: Steepest Descents converged to Fmax 250 in 61 steps Potential Energy = 4.6094102e+04 Maximum force = 2.4543298e+02 on atom 1 Norm of force = 7.5803179e+03 Is this a reasonable value for FMax? Thanks again for your help. Darrell Date: Thu, 16 Jul 2009 07:15:12 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5f0bc0.4020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, I do not do any equilibration, I only do energy minimization as in the GROMACS Tutorial for Solvation Study of Spider Toxin Peptide. Please let me know if I need to do equilibration and what is the difference between energy minimization and equilibration as this is not clear to me. Did the EM converge satisfactorily? What was Fmax? Unlike EM, equilibration is an MD process; for a protein system, one generally position-restrains the protein and allows the surrounding solvent to optimize around the structure. -Justin Here is an mdp file for a run that actually completed successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =1 nstcomm =100 nstxout =100 ;nstvout=1000 nstfout =0 nstlog =100 nstenergy =100 nstlist =100 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 And here is a copy of an mdp file for a run that did not complete successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =3 nstcomm =500 nstxout =500 ;nstvout=1000 nstfout =0 nstlog =500 nstenergy =500 nstlist =500 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Please let me know what you think might be the problem. Thanks Darrell Date: Thu, 16 Jul 2009 09:47:49 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5e6aa5.4040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, Yes, I know that the box dimensions are defined in the last line of the .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm in the .gro file. OK. I looked through my .gro file to ensure none of the atoms had coordinates outside the 38x38x38 box. While I was reviewing the file I did notice that some coordinates had negative values, slightly negative, but negative
Re: [gmx-users] Segmentation Fault (Address not mapped)
darre...@ece.ubc.ca wrote: Hi Justin, Thanks for the explanation of the difference between EM equilibration. Since in my model, I: (i) only have the graphene sheet and ammonia molecules spaced reasonably far apart from each other (1332 NH3 molecules in a 38x38x38 box) and from the graphene sheet (distance between the closest ammonia molecule and the graphene sheet is greater than the molecular diameter of ammonia - maybe this is too close and could be causing my problem?); (ii) freeze the graphene sheet; I am thinking equilibration is not required in my model. Please let me know if you think I still need to perform equilibration. Yes, the EM did converge satisfactorily. Here is the output from EM: Steepest Descents converged to Fmax 250 in 61 steps Potential Energy = 4.6094102e+04 Maximum force = 2.4543298e+02 on atom 1 Norm of force = 7.5803179e+03 Is this a reasonable value for FMax? Your Fmax looks fine. Why is it necessary to freeze the graphene sheet? Why not use position restraints (to rule out funky behavior of being frozen)? Did you ever obtain a trajectory with enough frames that you could watch? What happened? -Justin Thanks again for your help. Darrell Date: Thu, 16 Jul 2009 07:15:12 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5f0bc0.4020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, I do not do any equilibration, I only do energy minimization as in the GROMACS Tutorial for Solvation Study of Spider Toxin Peptide. Please let me know if I need to do equilibration and what is the difference between energy minimization and equilibration as this is not clear to me. Did the EM converge satisfactorily? What was Fmax? Unlike EM, equilibration is an MD process; for a protein system, one generally position-restrains the protein and allows the surrounding solvent to optimize around the structure. -Justin Here is an mdp file for a run that actually completed successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =1 nstcomm =100 nstxout =100 ;nstvout=1000 nstfout =0 nstlog =100 nstenergy =100 nstlist =100 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 And here is a copy of an mdp file for a run that did not complete successfully: title =Graphene ;warnings =10 cpp =cpp ;define =-DPOSRES constraints =none integrator =md dt =0.002 ; ps nsteps =3 nstcomm =500 nstxout =500 ;nstvout=1000 nstfout =0 nstlog =500 nstenergy =500 nstlist =500 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section freezes graphene lattice energygrps = Grph NH3 energygrp_excl = Grph Grph freezegrps = Grph ; Freeze graphene lattice freezedim = Y Y Y; in all directions Tcoupl =berendsen tau_t =0.50.5 tc-grps =NH3Grph ref_t =300300 ;coupl = parrinello-rahman ;tau_p = 1.5 ;compressibility = 1.3 ;ref_p = 0.061 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Please let me know what you think might be the problem. Thanks Darrell Date: Thu, 16 Jul 2009 09:47:49 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a5e6aa5.4040...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, Yes, I know that the box dimensions are defined in the last line of the .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm in the .gro file. OK. I looked through my .gro file to
Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system
Thank you Justin, I have tried to just solvate the peptide in water box using genbox command and spc216 water Then I have used the Energy Min mdp file form your tutorial (I have been folowing your tutorial for couple of days, the difference is that I want to put my segment on top of the membrane between the head groups of phospholipids). The DMPC box is stable, but I have trouble with 14aa peptide. It seems that is is unstable, I have made NH2 and COOO termini, maybe this is the problem? The results of EM for peptide in water: Step= 786, Dmax= 6.3e-03 nm, Epot= -1.37798e+06 Fmax= 7.60491e+02, atom= 67 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 787 steps Potential Energy = -1.3779814e+06 Maximum force = 7.6049121e+02 on atom 67 Norm of force = 1.8584177e+01 Then I run mdrun using mdp file that we use usually in our lab, and system crashed with LINCS warnings after 75 steps. But when I use the mdp file that is in EM section of your tutorial and change integrator = md. The peptide in water system is running without any warnings up till step 300. step 300, Warning: 1-4 interaction between 54 and 59 at distance 2.342 which is larger than the 1-4 table size 2.200 nm What settings would you recommend for MD runs in mdp files? Could you explain from your tutorial: How to Reduce the charges on the H atoms (all the way to zero, if necessary) Restore the charges before continuing And how Add [ exclusions ] within the topology between H and phosphate O atoms Remove the exclusions before continuing Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system
Kirill Bessonov wrote: Thank you Justin, I have tried to just solvate the peptide in water box using genbox command and spc216 water Then I have used the Energy Min mdp file form your tutorial (I have been folowing your tutorial for couple of days, the difference is that I want to put my segment on top of the membrane between the head groups of phospholipids). The DMPC box is stable, but I have trouble with 14aa peptide. It seems that is is unstable, I have made NH2 and COOO termini, maybe this is the problem? So, to clarify, you are embedding a peptide within the headgroups of a bilayer, not diffusing in water above the bilayer? What method are you using to delete overlapping lipids? InflateGRO? Setting those termini should not be the problem, in and of itself. The results of EM for peptide in water: Step= 786, Dmax= 6.3e-03 nm, Epot= -1.37798e+06 Fmax= 7.60491e+02, atom= 67 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 787 steps Potential Energy = -1.3779814e+06 Maximum force = 7.6049121e+02 on atom 67 Norm of force = 1.8584177e+01 That all looks quite good. Then I run mdrun using mdp file that we use usually in our lab, and system crashed with LINCS warnings after 75 steps. Can you post that .mdp file? But when I use the mdp file that is in EM section of your tutorial and change integrator = md. The peptide in water system is running without any warnings up till step 300. Don't. That file is for EM, with every other setting at default, which, IIRC, will not be appropriate for running MD. step 300, Warning: 1-4 interaction between 54 and 59 at distance 2.342 which is larger than the 1-4 table size 2.200 nm What settings would you recommend for MD runs in mdp files? Many settings depend on the force field model chosen. I can't make such a generic recommendation. Are you applying any position restraints to the protein to allow the lipids to pack around it? If you have voids around your lipid head groups, are you applying position restraints to the lipid head groups to allow water to soak in? Have you watched the output trajectory to see where things are falling apart? Could you explain from your tutorial: Note that the following comments are intended when there are voids around the lipid headgroups, or you specifically note that headgroups are collapsing in on themselves for specific lipids like POPE and POPG. They are not a generic solution for LINCS problems or other system collapses. Just a disclaimer for the archive :) How to Reduce the charges on the H atoms (all the way to zero, if necessary) Restore the charges before continuing Set the charge = 0.000 for H atoms in the lipid topology. This should not affect you; DMPC should not hydrogen bond within itself. And how Add [ exclusions ] within the topology between H and phosphate O atoms Remove the exclusions before continuing Make an [ exclusions ] directive and enter the atom numbers of the corresponding atoms. Chapter 5 is your friend here. Also not likely to be useful in your case, for the same reason above. -Justin Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] params for g_cluster and g_clustsize
Dmitri Dubov skrev: Thanks, David. Sorry, maybe my questions were too fuzzy. They concern the definition of cluster in these codes. 1) When we estimate through single linkage whether the structure belongs to the cluster we should find the smallest distance between any element of the structure and any element of cluster, then compare this distance with the cutoff value. I don't understand how this cutoff value may have root mean square deviation feature. The rmsd is given in nm, and if the rmsd falls below the cutoff (also given in nm, of course) the two frames are part of the same cluster when single lincage is used for g_cluster. 2) To my knowledge the g_clustsize uses the same single linkage algorithm for cluster construction. If so, there should be the similar cut-off parameter. The -cut option looks like this one. But very different default values of these parameters (cutoff=0.1 in g_cluster and cut=0.35 in g_clustsize) are doubted to me. Here's what I believe you've not quite grasped: g_cluster clusters *frames* in a trajectory, generating groups of structures; g_clustsize clusters atoms/molecules *within each frame*. That said, the low default cutoff for g_cluster makes it less likely that you will end up with all frames in the same cluster, and the higher default cut-off for g_clustsize is the typical hydrogen bond length and is useful for finding water clusters, e.g. droplets in vacuo. These two questions may be reformulated to single one: If I would apply these two codes (using single linkage with default values) to the same system how different would be the cluster partitions? One would be clusters containing frames, the other clusters containing atoms/molecules. They are used for completely different things. /Erik Thanks one more. Dmitri Dmitri Dubov wrote: Dear gmx'ers, Could you explain me the following points in manuals for g_cluster and g_clustsize programs? 1) Manual for g_cluster: single linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff... Other options... -cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor What does RMSD mean here? Root mean square deviation. Typical for proteins. 2) Manual for g_clustsize: -cut real 0.35 Largest distance (nm) to be considered in a cluster Is there any difference between -cut and -cutoff in g_cluster above? These are two different programs, unfortunately not sharing any code. Thanks. Dmitri ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] minimzation problem with a heterogeneous system
Hello, I have a configuration in which half of the box is liquid water and the other half is ice. This configuration is the output of another simulation in which the mentioned config worked (and still works fine). But when I start minimizing it (I started minimization since my first round of MD run crashed due to messages indicative of clashes). But minimation ends with the following message: Steepest Descents: Tolerance (Fmax) = 1.0e-06 Number of steps= 50 Step=1, Dmax= 1.0e-01 nm, Epot= 6.09464e+11 Fmax= 1.31718e+14, atom= 2938 Step=2, Dmax= 1.2e-01 nm, Epot= 1.15027e+09 Fmax= 2.00242e+11, atom= 2576 Step=3, Dmax= 1.4e-01 nm, Epot= 1.56529e+08 Fmax= 2.20702e+09, atom= 11062 t = 0.004 ps: Water molecule starting at atom 16078 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=4, Dmax= 1.7e-01 nm, Epot= 2.11002e+10 Fmax= 5.75671e+13, atom= 14986 t = 0.005 ps: Water molecule starting at atom 14902 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=5, Dmax= 8.6e-02 nm, Epot= 1.22915e+07 Fmax= 4.57843e+07, atom= 6280 t = 0.006 ps: Water molecule starting at atom 15952 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=7, Dmax= 5.2e-02 nm, Epot= 5.50887e+06 Fmax= 1.19611e+08, atom= 7348 Step=8, Dmax= 6.2e-02 nm, Epot= 4.29974e+06 Fmax= 1.39548e+07, atom= 12066 Step=9, Dmax= 7.5e-02 nm, Epot= 1.93270e+06 Fmax= 2.81542e+07, atom= 7204 t = 0.010 ps: Water molecule starting at atom 7300 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 26, Dmax= 1.4e-06 nm, Epot= 2.53306e+06 Fmax= 8.74996e+06, atom= 15953 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1e-06 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 27 steps, but did not reach the requested Fmax 1e-06. Potential Energy = 1.9327006e+06 Maximum force = 2.8154184e+07 on atom 7204 Norm of force = 4.1820662e+05 I checked the output .pdb files, and they show box is cracking from the position of the ice-water interface! Also, the ice part looks like a complete mess! (like it's not going to be ice anymore). I checked the .itp file to make sure are the variables are correct. Nothing looked wrong to me. I checked the mailing list about minimization. Just remember this water model is not flexible. Regards, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: July 16, 2009 12:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] making a box of water Payman Pirzadeh wrote: You were right! The dimensions of the box are zero in the .gro file. Should I change them to the values I have? Set them using editconf Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] How does pdb2gmx assign protonation in default condition?
Hi Justin, It seems that pdb2gmx determines the hydrogen position based on the start structure. In this case, hydrogens are added for an optimal hydrogen bond network. However, I am still wondering whether this for one-conformation optimized hydrogen position will be inappropriate for the rest of protein conformations. Actually, I noticed a questionable hydrogen assignment in the catalytic His residue of the enzyme, and yes, I can correct this if related references are available. But for others, I'm not sure they could be in correct state and how largely the hydrogen position will affect the structure dynamics. Maybe I should compare the MD trajectories from two different assignments and figure out this problem. Anyway, thank for your precious help. Best wishes Liu Ji Institute of Bioengineering Zhejiang University, China On 7/16/09, Justin A. Lemkul jalem...@vt.edu wrote: Liu Ji wrote: Hi all, I have a question about how pdb2gmx determines the protonation of the His residue in default. To best of my knowledge, His usually has its ND1 nitrogen free in un-protonated state, which might equal to the HISB presents in pdb2gmx. However, when I am treating pdb files by pdb2gmx without specifing exact state of His, the resulting structure contains both HISA (NE2 free) and HISB (ND1 free) state as something listed below, There are 1155 hydrogen bonds Will use HISB for residue 151 Will use HISB for residue 218 Will use HISB for residue 368 Will use HISA for residue 425 Will use HISB for residue 449 I am assuming that the hydrogen has been added in consideration of steric interaction, however, does this assignment violate the common knowledge? I can't find any references about this issue and am not sure how large influence will be generated. So can you give me any suggestions? Thanks a lot. Quoting from pdb2gmx -h: ...for HIS the proton can be either on ND1 (HISA), on NE2 (HISB) or on both (HISH). By default these selections are done automatically. For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively. -Justin Liu Ji Institute of Bioengineering Zhejiang University, China ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 mailing listgmx-users@gromacs.org http://lists.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
Re: [gmx-users] minimzation problem with a heterogeneous system
Payman Pirzadeh wrote: Hello, I have a configuration in which half of the box is liquid water and the other half is ice. This configuration is the output of another simulation in which the mentioned config worked (and still works fine). But when I start minimizing it (I started minimization since my first round of MD run crashed due to messages indicative of clashes). But minimation ends with the following message: Steepest Descents: Tolerance (Fmax) = 1.0e-06 Number of steps= 50 Step=1, Dmax= 1.0e-01 nm, Epot= 6.09464e+11 Fmax= 1.31718e+14, atom= 2938 Step=2, Dmax= 1.2e-01 nm, Epot= 1.15027e+09 Fmax= 2.00242e+11, atom= 2576 Step=3, Dmax= 1.4e-01 nm, Epot= 1.56529e+08 Fmax= 2.20702e+09, atom= 11062 t = 0.004 ps: Water molecule starting at atom 16078 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=4, Dmax= 1.7e-01 nm, Epot= 2.11002e+10 Fmax= 5.75671e+13, atom= 14986 t = 0.005 ps: Water molecule starting at atom 14902 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=5, Dmax= 8.6e-02 nm, Epot= 1.22915e+07 Fmax= 4.57843e+07, atom= 6280 t = 0.006 ps: Water molecule starting at atom 15952 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step=7, Dmax= 5.2e-02 nm, Epot= 5.50887e+06 Fmax= 1.19611e+08, atom= 7348 Step=8, Dmax= 6.2e-02 nm, Epot= 4.29974e+06 Fmax= 1.39548e+07, atom= 12066 Step=9, Dmax= 7.5e-02 nm, Epot= 1.93270e+06 Fmax= 2.81542e+07, atom= 7204 t = 0.010 ps: Water molecule starting at atom 7300 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 26, Dmax= 1.4e-06 nm, Epot= 2.53306e+06 Fmax= 8.74996e+06, atom= 15953 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1e-06 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 27 steps, but did not reach the requested Fmax 1e-06. Potential Energy = 1.9327006e+06 Maximum force = 2.8154184e+07 on atom 7204 Norm of force = 4.1820662e+05 I checked the output .pdb files, and they show box is cracking from the position of the ice-water interface! Also, the ice part looks like a complete mess! (like it's not going to be ice anymore). I checked the .itp file to make sure are the variables are correct. Nothing looked wrong to me. I checked the mailing list about minimization. Just remember this water model is not flexible. All we can say is the something is broken with your model or initial configuration. Simplify it into small, homogeneous systems until you can diagnose the source of the problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
