[gmx-users] the ligang topology
Dear, The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?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/Support/Mailing_Lists/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/Support/Mailing_Lists
Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
Mark, I've used that dimensions in accordance to some literature where the same membrane-mimicking simulation were performed. I've tried to rise cutoffs and dicrease integration step but my system have been stil crashed during npt. I'm using pcoupl= Parrinello-Rahman wich I've found in the KALP tutorial because I have not found the same npt example file in the Biphastic tutorial :) Could you advise me another p_coup algorithm for my Ccl4 system? James -- Forwarded message -- From: Mark Abraham mark.abra...@anu.edu.au Date: 2012/2/15 Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer To: Discussion list for GROMACS users gmx-users@gromacs.org On 15/02/2012 4:45 PM, James Starlight wrote: Mark, due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :) I want prevent such expansion of my system by increasing of pressure and/ or compressibility but I have not found exact sollution yet. Your system is dangerously small for those cut-offs if your initial density is not correct for your model physics. Your y and z dimensions only just contain a full cut-off sphere. You should also make sure you are following the advice about choice of P-coupling algorithm in manual 3.4.9, and consider using a very small integration time step. I remain unconvinced by this thread that you have generated a starting configuration that does not have atomic clashes. Mark James 2012/2/14 Mark Abraham mark.abra...@anu.edu.au On 14/02/2012 11:01 PM, James Starlight wrote: This also was solved by the some extra minimisation steps. I've forced with another problem :D During npt equilibration my system have slightly expanded so my desired volume and density were perturbed. I've noticed the below options in npt wich could help me ref_p= 1 1 compressibility = 4.5e-5 i'm using this compressibility value because I'm modelling the lipid-like environment so I think that I must increase pressure. Could you remind me the dependence of pressure from density and volume for liquids ? :) Your forcefield, simulation cell contents and .mdp settings will determine the equilibrium density. Whether you need to do anything depends on whether you've made a statistically significant post-equilibration measurement of your average density. Haphazardly increasing the reference pressure for the coupling will reduce the volume, but now you are simulating at that pressure. See http://www.gromacs.org/Documentation/Terminology/Pressure for background info. Mark James 2012/2/14 James Starlight jmsstarli...@gmail.com It seems that I've fixed that problem by reduce vdv radii for Cl during defining of my box Eventually I've obtained box with the desired density than I've delete vdvradii.dat for my wor dir by when I've launched equilibration I've oibtained Fatal error: Too many LINCS warnings (1598) If you know what you are doing you can adjust the lincs warning threshold in your mdp file I've never seen this before I'm using 1.o cutoff for pme and 1.4 for vdv my LINKS parameters are ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy How I could solve it? James 2012/2/14 James Starlight jmsstarli...@gmail.com Mark, I've checked only density value with 500 molecules Ccl4 I have density that is twisely less that I need ( in accordance to the literature ). Also I've checked my box visually and found that the box is not properly tightly packed so I dont know why genbox didnt add some extra mollecules :( In other words I wounder to know if there is any way to add some extra molecules to the pre defined box to make my system more tighly packed ( to short distance between existing molecules and place new ones in the new space ) ? James 2012/2/14 Mark Abraham mark.abra...@anu.edu.au On 14/02/2012 4:57 PM, James Starlight wrote: Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been added Added 0 molecules (out of 200 requested) of Cl4 ... then there are no gaps large enough to insert your molecules. Either make gaps, or check out genbox -h for advice on defining the radii. also I've tried
[gmx-users] BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory
Hi! I'm trying to run a mdrun-gpu simulation on a 64-bit Ubuntu system. I'm using a 15GB GTX 580 NVIDIA GPU card with all the appropriate drivers and cuda toolkit. However, when I run the command: mdrun-gpu -s inpufile.tpr -c inputfile.gro -x outputfile.xtc -g outputfile.log -nice - 0 I get the following error message: BornSum: cudaMalloc in CUDAStream::Allocate failed out of memory What is the problem? Is my 15GB GPU card insufficient for my 138596 atom system? Appreciate any help, Adam-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Water Shell Density
Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_select -select
Hello, I am trying to make an dynamic index file of the hydration shell of my protein (hopefully using it with other gromacs tools). I am considering up to 10A from protein as the distance needed for my selection. I am using g_select with the following format: g_select -f traj.xtc -s traj.tpr -on hydrationlayer -n -seltype res_com -select 'SOL within 10 of protein' but I get error messages about syntax. How can I select water molecules within 10A of my protein then? Best, Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] charmm27 in gromacs
In a nutshell, yes dihedral type 2 is for the IMPR charmm dihedrals and 9 is for the normal dihedrals. I think David or someone else added code to specifically support charmm dihedrals in this way. On 2012-02-14 09:32:37PM -0600, Tom wrote: Dear Gmx Developer or Users, Can anyone explain which section is for the parameters of improper dihedral angle on the file of ffbonded.itp ? On the file of ffbonded.itp, there is not any comment to differentiate the proper and improper dihedral angle. E.g. on thie file of ffbonded.itp in the directory of charmm27.ff There are two sections about dihedral angle: [ dihedraltypes ] ; i j k l funcphi0cp mult C CT1 NH1 C * 9* 180.00 0.8368 1 .. [ dihedraltypes ] ; i j k l funcq0 cq CPB CPA NPH CPA* 2* 0. 174.0544 .. There is also no explaination the explaination about the function type 2. It seems difficult for users to edit the parameters. Thanks for the explainations! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_select -select
On 16/02/2012 6:15 AM, Paymon Pirzadeh wrote: Hello, I am trying to make an dynamic index file of the hydration shell of my protein (hopefully using it with other gromacs tools). I am considering up to 10A from protein as the distance needed for my selection. I am using g_select with the following format: g_select -f traj.xtc -s traj.tpr -on hydrationlayer -n -seltype res_com -select 'SOL within 10 of protein' but I get error messages about syntax. How can I select water molecules within 10A of my protein then? Check out help examples within g_select, and remember that GROMACS doesn't work in Angstroms. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
On 16/02/2012 1:45 AM, James Starlight wrote: Mark, I've used that dimensions in accordance to some literature where the same membrane-mimicking simulation were performed. I've tried to rise cutoffs Don't, that breaks your model physics and makes it even more likely you will encounter problems with the system dimensions becoming too small for the cut-off! and dicrease integration step but my system have been stil crashed during npt. I'm using pcoupl= Parrinello-Rahman wich I've found in the KALP tutorial because I have not found the same npt example file in the Biphastic tutorial :) So you're following some other work and not copying their equilibration protocol and/or model physics? Could you advise me another p_coup algorithm for my Ccl4 system? There's only two choices available. Manual 3.4.9 specifically warns against one of them for equilibration. What is there to say? You should be sure to construct a simple case and get the model physics validated. For the moment, forget about all the stuff where you were struggling to insert more CCl4 into a box with CCl4 (probably creating a far-from-equilibrium starting configuration). Don't try to learn to run on stilts while shaving. Learn to shave, then to walk on stilts, then to run, then start combining them. Mark James -- Forwarded message -- From: *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Date: 2012/2/15 Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org On 15/02/2012 4:45 PM, James Starlight wrote: Mark, due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :) I want prevent such expansion of my system by increasing of pressure and/ or compressibility but I have not found exact sollution yet. Your system is dangerously small for those cut-offs if your initial density is not correct for your model physics. Your y and z dimensions only just contain a full cut-off sphere. You should also make sure you are following the advice about choice of P-coupling algorithm in manual 3.4.9, and consider using a very small integration time step. I remain unconvinced by this thread that you have generated a starting configuration that does not have atomic clashes. Mark James 2012/2/14 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 14/02/2012 11:01 PM, James Starlight wrote: This also was solved by the some extra minimisation steps. I've forced with another problem :D During npt equilibration my system have slightly expanded so my desired volume and density were perturbed. I've noticed the below options in npt wich could help me ref_p= 1 1 compressibility = 4.5e-5 i'm using this compressibility value because I'm modelling the lipid-like environment so I think that I must increase pressure. Could you remind me the dependence of pressure from density and volume for liquids ? :) Your forcefield, simulation cell contents and .mdp settings will determine the equilibrium density. Whether you need to do anything depends on whether you've made a statistically significant post-equilibration measurement of your average density. Haphazardly increasing the reference pressure for the coupling will reduce the volume, but now you are simulating at that pressure. See http://www.gromacs.org/Documentation/Terminology/Pressure for background info. Mark James 2012/2/14 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com It seems that I've fixed that problem by reduce vdv radii for Cl during defining of my box Eventually I've obtained box with the desired density than I've delete vdvradii.dat for my wor dir by when I've launched equilibration I've oibtained Fatal error: Too many LINCS warnings (1598) If you know what you are doing you can adjust the lincs warning threshold in your mdp file I've never seen this before I'm using 1.o cutoff for pme and 1.4 for vdv my LINKS parameters are ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to
[gmx-users] how to interpret tilt from g_helixorient?
Hi all I'm also having trouble with g_helixorient and the data it is giving me. My desired end goal is to track the average tilt of a helix compared to the global Z-axis, but a change in the tilt of the helix over time to its reference structure (frame 0) will suffice. How exactly do I interpret the tilt angles from g_helixorient? If I specify 4 CA atoms in the center of my helix, it seems to give me a running average of some sort with 0 angle angle 0. What is this angle in relation to? -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] in vacu simulation
Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? Thanks for your guidence, Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Water Shell Density
Probably you can use g_rdf -surf to get the surface based g(r) for water molecules, since g(r) is the local_density divided by the average_density, then local_density=g(r)_surf*average_density, which is a function of distance from the surface. Jianguo From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, 16 February 2012, 3:01 Subject: [gmx-users] Water Shell Density Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] the ligang topology
This paper has used united atoms for -CF3 and -CF2: Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309. Another way is to use ATB to generate the topology, but I am not sure if it can deal with fluorine atom. http://compbio.biosci.uq.edu.au/atb/ Jianguo From: xiaojiong xiaoji...@zju.edu.cn To: gmx-users@gromacs.org Sent: Wednesday, 15 February 2012, 19:35 Subject: [gmx-users] the ligang topology Dear, The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?Thanks! -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: charmm27 in gromacs
Got it. Thanks a lot for the help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] g_spatial index file
Hi, I used g_select to choose the hydration shell molecules of my protein from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to feed the generated index file into g_spatial to calculate the SDF of solvent around my protein. However, when I feed this into the g_spatial, it lists 1500 group and my protein. How can I tell the command to use the 1500 groups to calculate the SDF? Or can I specify a dynamic selection when I run the g_spatial? sth like resname SOL and within 1.0 of protein? Best, Paymon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). Sure, but reading the documentation is usually a better idea than making assumptions :) The underlying reason for this behaviour is that it is much easier for the person writing the code to have one parameter that occasionally has a special meaning when it takes a nonsense value (like rc=0) then it is to have a slew of parameters that have to be managed when they are input (and checked, and documented) and then possibly passed through a cascade of functions (lots of bureaucracy and chances to make errors) before they are used. The alternative costs the programmer more time. In an ideal world there would be an infinite amount of such time, but given the amount most people are prepared to pay for scientific software, that time is severely limited. And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? Efficiency, like I said in the first post in this thread. Given that your force field was parametrized with given cut-offs for the condensed phase, to what purpose do you wish to calculate in vacuo? The perturbation from calculating in vacuo will be much larger than the perturbation from the use of infinite cut-offs. 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] g_spatial index file
On 16/02/2012 3:03 PM, Paymon Pirzadeh wrote: Hi, I used g_select to choose the hydration shell molecules of my protein from a trajectory of 15ns saved every 10ps (1500 frames). Now I want to feed the generated index file into g_spatial to calculate the SDF of solvent around my protein. However, when I feed this into the g_spatial, it lists 1500 group and my protein. How can I tell the command to use the 1500 groups to calculate the SDF? You will need to use something like a shell script to loop over each group and match it with its frame. See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts for clues. Or can I specify a dynamic selection when I run the g_spatial? sth like resname SOL and within 1.0 of protein? Not yet. This kind of functionality will exist in GROMACS 5.0 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
On 15 February 2012 23:05, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). Sure, but reading the documentation is usually a better idea than making assumptions :) The underlying reason for this behaviour is that it is much easier for the person writing the code to have one parameter that occasionally has a special meaning when it takes a nonsense value (like rc=0) then it is to have a slew of parameters that have to be managed when they are input (and checked, and documented) and then possibly passed through a cascade of functions (lots of bureaucracy and chances to make errors) before they are used. The alternative costs the programmer more time. In an ideal world there would be an infinite amount of such time, but given the amount most people are prepared to pay for scientific software, that time is severely limited. And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? Efficiency, like I said in the first post in this thread. Given that your force field was parametrized with given cut-offs for the condensed phase, to what purpose do you wish to calculate in vacuo? The perturbation from calculating in vacuo will be much larger than the perturbation from the use of infinite cut-offs. Thank you. I am looking at potential of a single molecule in vacu for heat of vap purposes at different temperatures by changing ref_temp and gen_temp for each run. 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Thanks, J. N. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] in vacu simulation
On 16/02/2012 3:14 PM, Juliette N. wrote: On 15 February 2012 23:05, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). Sure, but reading the documentation is usually a better idea than making assumptions :) The underlying reason for this behaviour is that it is much easier for the person writing the code to have one parameter that occasionally has a special meaning when it takes a nonsense value (like rc=0) then it is to have a slew of parameters that have to be managed when they are input (and checked, and documented) and then possibly passed through a cascade of functions (lots of bureaucracy and chances to make errors) before they are used. The alternative costs the programmer more time. In an ideal world there would be an infinite amount of such time, but given the amount most people are prepared to pay for scientific software, that time is severely limited. And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? Efficiency, like I said in the first post in this thread. Given that your force field was parametrized with given cut-offs for the condensed phase, to what purpose do you wish to calculate in vacuo? The perturbation from calculating in vacuo will be much larger than the perturbation from the use of infinite cut-offs. Thank you. I am looking at potential of a single molecule in vacu for heat of vap purposes at different temperatures by changing ref_temp and gen_temp for each run. So it's much more bureaucracy every nstlist0 steps to take your N atoms and look at their distance from the other N-1 atoms and make lists of which ones are inside rc than it is to just compute them all every step and know that if they're further than rc then the effect is tiny. For small enough N, the later is guaranteed to be faster... 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the
Re: [gmx-users] in vacu simulation
Thanks. That was a new thing for me to learn. On 15 February 2012 23:19, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 3:14 PM, Juliette N. wrote: On 15 February 2012 23:05, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 2:08 PM, Juliette N. wrote: On 15 February 2012 21:00, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/02/2012 12:22 PM, Justin A. Lemkul wrote: Juliette N. wrote: Hi all, I am trying to run simulation in vaccum using the the changes shown below to the usual mdp file. pbc = no ;coulombtype = PME ;vdw-type= Shift ;Cut-offs rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 ns_type = simple Can anyone help me with some short questions please? 1- for pbc=no, I need to comment ;coulombtype = PME ;vdw-type= Shift so it defaults to vdw-type = Cut-off which are not suitable algorithms. Is using cut offs justified for in vacu runs? Plain truncations in condensed-phase systems lead to artifacts. Neither of those conditions apply here, as you're using infinite cutoffs. 2- I am not clear about using infinite cutoffs. Why one refers to infinite cutoffs when rlist = 0 rcoulomb = 0 rvdw = 0 ? My understanding is that this settings means zero cutoff i.e no interaction is calculated. Why does this setting refer to infinite rc? That's the way the code works. There are various parameters that can be set to -1, for instance, and that doesn't mean quantities are calculated every -1 steps ;) Setting cutoffs to zero in this manner mean *all* interactions are calculated, not none. Prove it to yourself with a zero-step MD run. The nonbonded energy terms will not be zero, as they would in the case that no interactions would be calculated. Or read about pbc=no in manual section 3.4.9 like I suggested Juliette do earlier this week... Thanks Justin and Mark. I think you meant 7.3.9 which I did when you referred me to that. My problem was that I did not expect rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0 looked more equivalent to no interaction than infinite cutff off (all interactions). Sure, but reading the documentation is usually a better idea than making assumptions :) The underlying reason for this behaviour is that it is much easier for the person writing the code to have one parameter that occasionally has a special meaning when it takes a nonsense value (like rc=0) then it is to have a slew of parameters that have to be managed when they are input (and checked, and documented) and then possibly passed through a cascade of functions (lots of bureaucracy and chances to make errors) before they are used. The alternative costs the programmer more time. In an ideal world there would be an infinite amount of such time, but given the amount most people are prepared to pay for scientific software, that time is severely limited. And also I dont see why do we need to change rc to infinite. I mean if force fields dictate cutoffs based on a distance where nonbonded interactions are close enough to zero (negligible), what purpose use of infinite cutoff serve? Efficiency, like I said in the first post in this thread. Given that your force field was parametrized with given cut-offs for the condensed phase, to what purpose do you wish to calculate in vacuo? The perturbation from calculating in vacuo will be much larger than the perturbation from the use of infinite cut-offs. Thank you. I am looking at potential of a single molecule in vacu for heat of vap purposes at different temperatures by changing ref_temp and gen_temp for each run. So it's much more bureaucracy every nstlist0 steps to take your N atoms and look at their distance from the other N-1 atoms and make lists of which ones are inside rc than it is to just compute them all every step and know that if they're further than rc then the effect is tiny. For small enough N, the later is guaranteed to be faster... 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Thanks, J. N. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Placing ions in the specified positions
Dear Gromacs users! I've constructed my biphastic system with the water-ccl4-water layers where in the ccl4 layer I've placed my membrane protein. Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to mimick the 'positive-inside rule' (my protein consist of 5 Lys) of the membrane protein topology. How I could specify to place some ions in the desired possitions? As i understood the genion place ions in the random possitions so I've obtained 3 ions in the bottom and 2 in the upper layer. Thanks James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Placing ions in the specified positions
On 16/02/2012 6:13 PM, James Starlight wrote: Dear Gromacs users! I've constructed my biphastic system with the water-ccl4-water layers where in the ccl4 layer I've placed my membrane protein. Now I'd like to place addition 5 Cl ions to the bottow leafleat of water to mimick the 'positive-inside rule' (my protein consist of 5 Lys) of the membrane protein topology. How I could specify to place some ions in the desired possitions? As i understood the genion place ions in the random possitions so I've obtained 3 ions in the bottom and 2 in the upper layer. Make five holes by removing cunningly chosen water molecules reasonably spaced out. Add five plus a few extra Cl ions, and remove those that went to unsuitable locations. Equilibrate forever - but you were going to have to do this anyway! 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/Support/Mailing_Lists/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/Support/Mailing_Lists
