Re: [gmx-users] Center of mass motion removal

Hi Tuong Vy, There is no difference in practice except for raising the error. The developers can't try catching all possible foolish things people could try with an error. Also, if you think of fooling the program in this way, you may be assumed to know what you're doing (and why you wouldn't need

Re: [gmx-users] Volume of active site

Dear Erik, As per your suggestion I have tried gmx sasa -tv option to get the volume of the active site with help of a defined set of residues (17 residues) as defined in the index file. But for all systems, mutants and wild type enzymes have similar profile of volume throughout the simulation t

Re: [gmx-users] Center of mass motion removal

Dear Tsjerk and all, If I set up the comm-mode =None ( COM motion is not removed), i got the Warning : numerical rounding errors can lead to build up of kinetic energy of the COM and the simulation can not run. I think comm-mode =None and {comm-mode =Linear , nstcomm > nststeps) is similar meanin

Re: [gmx-users] Center of mass motion removal

Hi Tsjerk, So what different between nstcomm > nsteps case and comm-mode = none case? Because when I set this option (comm-mode = none), the dynamisc tpr file can not be run. It returned the error related to built up the kinetics energy. But it didn't with nstcomm > nsteps, the md still be performe

Re: [gmx-users] Center of mass motion removal

Hi Tuong Vy, Right. If COMM is removed every N steps and the simulation runs for M < N steps, then COMM will never actually be removed. Cheers, Tsjerk On Jun 3, 2015 4:44 AM, "Vy Phan" wrote: > Dear all, > I wonder when I set the comm-mode =Linear , and nstcomm > (frequency for COM motion remo

Re: [gmx-users] does gromos force field support implicit solvent?

Hi, Probably not - it wasn't parameterised for such usage, and any such re-deployment would require careful validation . Your background reading on your choice of model physics is your best guide to doing good physics. :-) Mark On Wed, 3 Jun 2015 07:55 Ming Tang wrote: > Dear gromacs experts,

[gmx-users] does gromos force field support implicit solvent?

Dear gromacs experts, I tried to use gromos 54a7 force field to calculate persistence length of a helix in implicit solvent, but got GB parameters missing errors. When I tried to modify the implicit_genborn_params section, I found there is not gbsa.itp file in gromos54a7.ff does gromos force f

[gmx-users] epsilon_r option

Dear all, I want to ask two questions about the epsilon_r and epsilon_rf option in mdp file to run CG simulation. If I do not specify 2 these option, the gromacs will return the default value (epsilon_r = 1 and epsilon_rf = 0). If the epsilon_r =15, is there any effect on the electrostatic interact

[gmx-users] Looking for FF parameters for bivalent metals and oxoguanine

I'm investigating several protein-DNA systems with AMBER 99SB force field . Some of them involve 8-oxoG lesions and metal-dependent enzymes. Is there any reliable calculated parameters for them or any reliable and reasonably quick way to derive them? -- Gromacs Users mailing list * Please searc

[gmx-users] epsilon-r

Dear Gromacs Users, I do not know how to set up the epsilon-r and epsilon-rf in simulation with spc model water. I set it as default value (epsilon-r =1 and epsilon-rf =0). Is it right? Thank you so much Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.

Re: [gmx-users] No default Ryckaert-Bell. types for proline

Thanks Justin, I have long been confused by atom names and types in Gromacs topology. I have just went through the manual again, and it confirms me that what we read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are atomtypes. In other words, what you have listed in the last e

[gmx-users] Center of mass motion removal

Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency for COM motion removal) > nststeps (maxinum number of steps), the MD simulation can be performed. I think the nstcomm > nsteps mean COM motion is not removed (the MD simulation can be not performed) Could somebody explai

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/2/15 8:51 PM, Kevin C Chan wrote: Thanks Justin, I'm sorry that I'm not clear with what do you mean by "so you can likely just use the same parameters in ffbonded.itp for this dihedral in the zwitterionic form". The Pro dihedral term for this torsion is the same, irrespective of whethe

[gmx-users] No default Ryckaert-Bell. types for proline

Thanks Justin, I'm sorry that I'm not clear with what do you mean by "so you can likely just use the same parameters in ffbonded.itp for this dihedral in the zwitterionic form". Also as I have mentioned before, when I look into the line 161, it refers to a dihedral term concerning (CD N CA C) whi

Re: [gmx-users] Tutorial site down

Dear Justin, I hope all thing will be on its road soon :) Tuong Vy 2015-06-02 23:12 GMT+09:00 Justin Lemkul : > > All, > > Yesterday we experienced a hardware failure on the server that hosts my > GROMACS tutorials. We are aware of the issue and are going to be setting > up a new server. The t

Re: [gmx-users] Alchemically Change 1-4 Interactions

On 6/2/15 2:07 PM, Eric Dybeck wrote: Hello All, I am attempting to alchemically change my solid small-molecule system from one forcefield to another using a series of linearly interpolated lambda states. For the bonds, angles, and dihedrals, a 'State A' and 'State B' can be specified in the t

[gmx-users] Hydrophobic interactions.

Hi all, I've been using gromacs for some time. But always carried out hydrophobic interactions for proteins using g_mindist. If I want to represent hydrophobic interactions in a better way, what is the best possible way? Regards BP. -- Gromacs Users mailing list * Please search the archive at h

[gmx-users] Alchemically Change 1-4 Interactions

Hello All, I am attempting to alchemically change my solid small-molecule system from one forcefield to another using a series of linearly interpolated lambda states. For the bonds, angles, and dihedrals, a 'State A' and 'State B' can be specified in the topology file which will linearly change th

Re: [gmx-users] Problem with mdrun on 8CPUs and 1GPU for gromacs 4.6.3

Hi, This is caused by an MPI rank failing to be able to get access to the GPU. Maybe this could happen if your ranks are not all actually on the same node? There would be an error message on stderr if your infrastructure hadn't swallowed it, but I don't know how to configure it to behave better.

Re: [gmx-users] GROMACS http download?

Hi, We currently don't have the infrastructure to make more than one source available. You can generally find the latest version archived at fossies.org ( http://fossies.org/search?q=gromacs&rd=%2Ffresh%2F&sd=0&ud=%2F&ap=no&ca=no&dp=0&si=0&sn=1&ml=30&dml=3), but I don't know of a more historical a

Re: [gmx-users] Microwave

It really depends on what level of theory you want to have in your simulation. If this is simple temperature increase due to GHz AC electric fields, GMX has the provisions already, and there's no need to patch anything. If you need magnetic fields and explicit secondary radiation, i.e. MD coupled w

[gmx-users] GROMACS http download?

I can't access the tar.gz at http://www.gromacs.org/Downloads because it is on FTP, which my (corporate) proxy blocks. Is there an http mirror where I can download these files? I need to download these: ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.5.tar.gz ftp://ftp.gromacs.org/pub/gromacs/grom

[gmx-users] Problem with mdrun on 8CPUs and 1GPU for gromacs 4.6.3

Dear Gromacs users, I'm trying to get the best performance out of a cluster which has for every node 8 CPUs and 1 GPU. To check it out, I run martini polarisable water system. Yet I have problems with it. While mdrun works for one MPI process, it crashes for 8 MPI processes and 1 GPU. Below is

[gmx-users] Tutorial site down

All, Yesterday we experienced a hardware failure on the server that hosts my GROMACS tutorials. We are aware of the issue and are going to be setting up a new server. The tutorials may end up on this new server or another; I haven't decided yet. For the next few days, the tutorials will be

Re: [gmx-users] g_hbond on trajectory

Thank you, Justin. Jennifer On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul wrote: > > > On 6/2/15 5:01 AM, Jennifer Vo wrote: > >> Dear All, >> I used g_hbond to analyze the possible hydrogen bonds between protein and >> solvent (water) over the trajectory with this command: >> g_hbond -s md-1.t

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

Hi Max, Thanks for the paper. This is helpful. -Dewey Ebert Maximilian wrote: > Hi Dewey, > maybe a little bit off topic but your description of the system reminded me > of a paper I read a couple of years ago. Do you know about the ABF method and > the work of Lamoureux et al? (http://pubs.acs.

Re: [gmx-users] fullerene crashes during energy minimization

Are you sure you are using the correct force field? Did you ignore any warning given by grompp before doing mdrun for energy minimization? Try altering the box size/ shape in the configuration file or and/or reduce the time step. If the problem still persists may be there is something wrong in the

Re: [gmx-users] Microwave

On 02/06/15 14:07, Justin Lemkul wrote: On 6/2/15 4:31 AM, Mostafa Javaheri wrote: Dear Justin, How could I simulate a membrane protein while there is microwave radiations in one direction e.g. in direction of z-axis? Should I change the delta-lambda delta-lambda is a free energy option.

Re: [gmx-users] g_hbond on trajectory

On 6/2/15 5:01 AM, Jennifer Vo wrote: Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdis

Re: [gmx-users] fullerene crashes during energy minimization

Dear Rahul, On Tue, Jun 2, 2015 at 1:08 PM, Rahul verma wrote: > Dear Gmx Users, > > I obtained topology files for fullerene from ATB website in order to > simulate > water confined in fullerene.However on energy minimization the fullerene > undergoes > complete structural changes.How should I t

Re: [gmx-users] Microwave

On 6/2/15 4:31 AM, Mostafa Javaheri wrote: Dear Justin, How could I simulate a membrane protein while there is microwave radiations in one direction e.g. in direction of z-axis? Should I change the delta-lambda delta-lambda is a free energy option. or Is this accessible via electric field

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 12:25 PM, Kevin C Chan wrote: pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter > 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) > 1: TIP4P TIP 4-point, recommended > 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) > 1: PRO-ZWITTERI

Re: [gmx-users] bend angles of a kink motif

On 6/1/15 12:19 PM, h.aliza...@znu.ac.ir wrote: Dear Users Can we calculate the bend angle of a kink motif in an alpha helix from a .xtc file? gmx angle calculates angles, as the name implies. There are also a number of programs that calculate helix properties. See the manual. -Justin

[gmx-users] fullerene crashes during energy minimization

Dear Gmx Users, I obtained topology files for fullerene from ATB website in order to simulate water confined in fullerene.However on energy minimization the fullerene undergoes complete structural changes.How should I take this up so that the structure of fullerene remains same during energy mini

Re: [gmx-users] Volume of active site

hello gromacs users its working i have calculated the volume and density of active site residues (in one group) but it gives value like time in ps volume density if i want to calculate the per residue wise change in volume and density is there any way. thanks in advance On Mon, Jun 1, 2015 at 10:

[gmx-users] g_hbond on trajectory

Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg The log file showed me: SER1

Re: [gmx-users] temperature problem

Hi, Runaway heating is the only useful feature of cutoff electrostatics. Use an actual model physics. Mark On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon wrote: > > > On 02/06/15 09:43, Lovika Moudgil wrote: > > Hi everyone > > > > > > I am having some problem in my md run .In my system temperatu

[gmx-users] Microwave

Dear Justin, How could I simulate a membrane protein while there is microwave radiations in one direction e.g. in direction of z-axis? Should I change the delta-lambda or Is this accessible via electric field option? If I have to use electric field option, should I patch the mdrun ( http://www.gro

Re: [gmx-users] temperature problem

On 02/06/15 09:43, Lovika Moudgil wrote: > Hi everyone > > > I am having some problem in my md run .In my system temperature of system > is abruptly increasing .I have done nvt for 50 picoseconds ..nd then using > it for further md simulation .I am not getting any error for this > temperature inc

[gmx-users] temperature problem

Hi everyone I am having some problem in my md run .In my system temperature of system is abruptly increasing .I have done nvt for 50 picoseconds ..nd then using it for further md simulation .I am not getting any error for this temperature increase .But when I plot temperature graph , temperat