[gmx-users] smd

Dear everyone， i want to use gromacs to perform the steered molecular dynamcs simulation. My system is the protein-ligand complex in the center of the box an i want to pull out of the ligand form the protein ative site. i have set the pbc in my mdp file. However, after simulation, i find

Re: [gmx-users] centering a protofibril in a box

Hi Adriana, Centering only shifts the positions. I guess you also want to put stuff back into the box and then make the molecules whole. You'll probably need several passes to get what you want. Cheers, Tsjerk On Nov 6, 2014 11:54 PM, "Justin Lemkul" wrote: > > > On 11/6/14 10:58 AM, Adriana G

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

<<< text/html; charset=UTF-8: Unrecognized >>> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://mai

Re: [gmx-users] Charmm to gromacs conversion for lipids

Dear Justin, Please check the atom section of "toppar_all36_lipid_cholesterol.str" file that I pasted below. * Toppar stream file for cholesterol. Stream following reading of * top_all36_lipid.rtf and par_all36_lipid.rtf !reference !Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. "Mol

Re: [gmx-users] Pressure Question

On Thu, 6 Nov 2014, Téletchéa Stéphane wrote: Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based "instantaneous pressure" (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulat

Re: [gmx-users] Umbrella sampling ignore hydrogen command -ignh

On 11/6/14 4:53 PM, Chris Papamitrou wrote: I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the pdb2gmx -f input.pdb -ignh -ter -o complex.gro

Re: [gmx-users] centering a protofibril in a box

On 11/6/14 10:58 AM, Adriana Garro wrote: Thanks Justin. I know it was not enough clear, it was because of my limited English proficiency. What I wanted (and want) to do is centering the first monomer of the protofibril in the box, so the protofibril would be shifted to the bottom part allowing

Re: [gmx-users] Version problem

I typed an extra space that shouldn't be there. $ find / -name mdrun* > mdrun_search On Thu, Nov 6, 2014 at 5:03 PM, Johnny Lu wrote: > can look for all files with name mdrun by > > $ find / -name mdrun * > mdrun_search > and then > $ cat mdrun_search > > > On Thu, Nov 6, 2014 at 7:25 AM, Erik

Re: [gmx-users] Version problem

can look for all files with name mdrun by $ find / -name mdrun * > mdrun_search and then $ cat mdrun_search On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund wrote: > Hi, > > 'which mdrun' only tells you the location of the mdrun you're currently > using and is no good here. How did you install 5.

[gmx-users] Umbrella sampling ignore hydrogen command -ignh

I am trying to perform a simulation regarding the effect that hydration has on tensile response for my system. When i looked into the umbrella sampling tutorial it said to create a start file using the pdb2gmx -f input.pdb -ignh -ter -o complex.gro command and was wondering what effect that the

Re: [gmx-users] Fwd: Re: Frequency dependent dielectric constant

On 2014-11-06 22:28, David van der Spoel wrote: Original Message Subject: Re: [gmx-users] Frequency dependent dielectric constant Date: Thu, 6 Nov 2014 16:23:34 -0500 From: Bharat Sharma To: sp...@xray.bmc.uu.se Hello Professor David, Sorry for sending you

Re: [gmx-users] How to exclude atoms within the same molecule from an rdf.

It's fairly "simple": generate a .tpr file with a nrexcl big enough to exclude "self-counts" and give it to g_rdf through the -s flag. João On Thu, Nov 6, 2014 at 8:42 PM, Stella Nickerson wrote: > I'm simulating a mixture of molecules (call them Molecules A, B, and C). > The rdf between A and

[gmx-users] Fwd: Re: Frequency dependent dielectric constant

Original Message Subject:Re: [gmx-users] Frequency dependent dielectric constant Date: Thu, 6 Nov 2014 16:23:34 -0500 From: Bharat Sharma To: sp...@xray.bmc.uu.se Hello Professor David, Sorry for sending you a private email. Thank you for your reply on foru

[gmx-users] How to exclude atoms within the same molecule from an rdf.

I'm simulating a mixture of molecules (call them Molecules A, B, and C). The rdf between A and B and between A and C both look fine, but the one between A and A is crazy-looking. I assume this is because it's comparing atoms within the same molecule. I can't figure out how to exclude atoms in the s

Re: [gmx-users] Frequency dependent dielectric constant

On 2014-11-06 19:33, Bharat Sharma wrote: Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. g_dielectric. Thank you. Bharat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala,

Re: [gmx-users] Frequency dependent dielectric constant

Hello, It's a friendly reminder if someone knows how to calculate. Please let me know. Thank you. Bharat -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/

[gmx-users] help for strange linear force in Pulling

Dear Gromacs User, I am using the pulling to pull two objects apart with Gomacs 4.6.5. To avoid the issues of half-box size limitation, i used direction_periodic to make two objects apart from each more than half-box-size distance. I just got the linear force: force change with time linearly. Th

Re: [gmx-users] problem in NPT equilibration

Dear Justin, Thanks for the clarification. I am currently doing the NVT step and after that I will move forward to the production md run. Regards, Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Pressure Question

If the problem of using a 11 bar simulation is as big as the problem of drawing conclusion from a single simulation, I guess I have to get a pressure closer to 1 bar. Thanks. On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu wrote: > I see. I'm using the V-rescaling thermostat in all simulations that I

Re: [gmx-users] Avg. Volume in NPT by Small Coupling Time

Assume sampling is sufficient in all stages of simulations. Will the berendsen barostat with this coupling constant give both the correct average volume and correct average pressure? (despite the distribution is not canonical) Will that average pressure change when I switch to NVT ensemble? Can I

Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500

On Thu, Nov 6, 2014 at 4:35 PM, Machtens, Jan-Philipp < j.macht...@fz-juelich.de> wrote: > Hi, > yes I will post that to redmine soon, but let me first clarify the issue, > since I tested some more conditions in the meantime. > (I realized that my trajectory had 1501 frames and the error occured w

Re: [gmx-users] centering a protofibril in a box

Thanks Justin. I know it was not enough clear, it was because of my limited English proficiency. What I wanted (and want) to do is centering the first monomer of the protofibril in the box, so the protofibril would be shifted to the bottom part allowing aggregate more and more monomers without havi

Re: [gmx-users] Pressure Question

I see. I'm using the V-rescaling thermostat in all simulations that I ran. I don't think I will use NPT for production run. I'm trying to get NVE production run in the end. If I use NVT production run, I will try to account for the effect of the thermostat (I'm not sure I can do that very well).

Re: [gmx-users] Avg. Volume in NPT by Small Coupling Time

Hi, I think that's fine for rapidly forcing the volume to be close to the right equilibrium value, with low fluctuations. Then switch to gentler NPT (or constant-volume) for making a proper observation of the pressure. Mark On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu wrote: > Hi. > > How to get

Re: [gmx-users] Pressure Question

Hi, Note that using the Berendsen thermostat in Gromacs adds defects for no gain, compared with the Bussi v-rescale thermostat. The latter *is* Berendsen, plus a stochastic term that produces the right energy and velocity distributions (unlike Berendsen). I'd give serious consideration to rejectin

[gmx-users] Avg. Volume in NPT by Small Coupling Time

Hi. How to get an accurate average volume for a system, such that the pressure will be at 1 bar in a subsequent NVT run using this average volume? Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) ? (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps).

Re: [gmx-users] Pressure Question

On Thu, Nov 6, 2014 at 12:39 PM, Johnny Lu wrote: > I was not offended by the suggestion. With a sufficiently large number of > water molecules, the protein would behave in the same way, under all three > ensembles. > Barostat and thermostat are artificial in some way. Biochemistry takes place

Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500

Hi, yes I will post that to redmine soon, but let me first clarify the issue, since I tested some more conditions in the meantime. (I realized that my trajectory had 1501 frames and the error occured when I choose more than 500 atoms, i.e. when the number of degrees of freedom becomes larger the

Re: [gmx-users] Pressure Question

That post in the amber mailing list was quite interesting. May be using a weak berendsen thermostat in NVT is fine for them. Thanks for sharing that. On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu wrote: > I was not offended by the suggestion. With a sufficiently large number of > water molecules, th

Re: [gmx-users] problem in NPT equilibration

On 11/6/14 8:46 AM, soumadwip ghosh wrote: Dear Justin, Thank you so much for your suggestion. I did the NPT equilibration with nxtout=500 and got 1.05 bar pressure along with the density of the system = 1009 Kg/m3, which is in agreement to the SPC/E water model. In additio

Re: [gmx-users] problem in NPT equilibration

Dear Justin, Thank you so much for your suggestion. I did the NPT equilibration with nxtout=500 and got 1.05 bar pressure along with the density of the system = 1009 Kg/m3, which is in agreement to the SPC/E water model. In addition, I got the cell volume fixed at 285 nm3, which

Re: [gmx-users] Charmm to gromacs conversion for lipids

On 11/6/14 8:38 AM, Venkat Reddy wrote: Dear Justin, Yes, the problem is with the blank line at the end of atomtypes.atp. Now its working fine. I have added the missing dihedral types from other sources. Thanks, I will fix that. I have compared the cholesterol CHARMM parameters that are co

Re: [gmx-users] Charmm to gromacs conversion for lipids

Dear Justin, Yes, the problem is with the blank line at the end of atomtypes.atp. Now its working fine. I have added the missing dihedral types from other sources. I have compared the cholesterol CHARMM parameters that are converted to gromacs format and original parameters from "toppar_all36_lipi

Re: [gmx-users] centering a protofibril in a box

On 11/6/14 6:13 AM, Adriana Garro wrote: Dear all, I am trying to center a protofibril in a box, but respect to its first monomer. (the result would be the protofibril shiftted to the botton of the box) I used trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb I d

Re: [gmx-users] Charmm to gromacs conversion for lipids

On 11/6/14 12:45 AM, Venkat Reddy wrote: Dear Justin, Thanks for the update. But unfortunately I couldn't find the parameters for cholesteryl oleate. So, I tried to convert again the parameters from CHARMM to GROMACS using these updated files: ./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_est

Re: [gmx-users] Tested and most compatible Gromacs version for Mac OS Leopard (10.5)

Hi, In principle, any Gromacs version will work on any Mac OS version, but the problem lies in getting a compiler toolchain that works correctly. Stock Apple compilers are based on clang, which doesn't support OpenMP, and would be outperformed by gcc if the linker in the binutils supported AVX SIM

Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500

Hi, IIRC some minor bugs were fixed, but a regression like that should be dealt with... please file at http://redmine.gromacs.org. Mark On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp < j.macht...@fz-juelich.de> wrote: > Dear all, > I observed that g_covar in Gromacs 5.0.2 segfaults at t

Re: [gmx-users] Minimization is not running

This is because you are using 4.6.5 provided by your OS, and it has been compiled assuming SSE4.1, but your machine is so old it only runs SSE2. When you find your 5.0.2 install, it will be probably compiled for SSE2. Mark On Thu, Nov 6, 2014 at 12:52 PM, wrote: > Dear all, > > I am just new to

Re: [gmx-users] Version problem

Hi, Well, you need to find out where you installed it (default /usr/local/bin). Using "which" or "locate" will only find the version from your OS distribution. Since you plan to use 5.0.2, you should uninstall the OS version using the package manager, to save yourself from further accidental confu

Re: [gmx-users] Version problem

Hi, 'which mdrun' only tells you the location of the mdrun you're currently using and is no good here. How did you install 5.0.2? The CMake files should tell you where installation directory is. Kind regards, Erik On 6 Nov 2014, at 11:43, sa...@physics.iisc.ernet.in wrote: > > tried "which m

[gmx-users] Minimization is not running

Dear all, I am just new to GROMACS, tried to install v5.0.2, although isntallation was successful, while running it is giving problem: I am just trying to do the lysozyme tutorial, however first energy minimization is not running, mdrun stopped with: === Reading file em.tpr, VERSION

Re: [gmx-users] Version problem

tried "which mdrun" showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded v5.0.2.tar.gz and used for installation. > try to find mdrun program by typing this command on terminal: > "which mdrun" > will show path of mdrun program where it located. > On Nov 6, 2014 4:01 PM, wro

Re: [gmx-users] md.log interpretation

I have tried running simulation with zero cutoff and zero nstlist and simple ns. That was very very slow, however. anyway thanks for the reply. On Nov 5, 2014 9:38 PM, "Mark Abraham" wrote: > Hi, > > I am not familiar with the implementation details, but I would assume there > is a dependency o

Re: [gmx-users] Pressure Question

I was not offended by the suggestion. With a sufficiently large number of water molecules, the protein would behave in the same way, under all three ensembles. Barostat and thermostat are artificial in some way. At least, even the diffusion coefficient is different in a force field paper that used

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

Dear Kester, The potential energy is highly positive in the first case and the force is enormous in the second case, so no wonder that they blow up. How did you prepare these systems? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physi

Re: [gmx-users] Version problem

try to find mdrun program by typing this command on terminal: "which mdrun" will show path of mdrun program where it located. On Nov 6, 2014 4:01 PM, wrote: > Dear Dr. Carsten Kutzner, > I am unable to find the "gmx5/bin/GMXRC" in my machine, > used 'locate' and 'find' to search the locatio

[gmx-users] centering a protofibril in a box

Dear all, I am trying to center a protofibril in a box, but respect to its first monomer. (the result would be the protofibril shiftted to the botton of the box) I used trjconv -f protofibril.pdb -n index.ndx -center -s protofibril.pdb -o test.pdb I did an index for the residues corresponding to

[gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500

Dear all, I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization step, if the group for the covariance analysis is bigger than 500 atoms, i.e. if the covariance matrix is bigger than 1500x1500. In my hands, this problem does not arise with g_covar 4.6.x. The results obtained f

[gmx-users] Tested and most compatible Gromacs version for Mac OS Leopard (10.5)

Dear Gromacs Users, Please suggest me latest gromacs version which will suit Mac OS Leopard (on Apple cluster) without having any problems. Can it be possible to use 5.0 Gromacs series for the same?. I searched in net and mailing list didn't found any reliable answer. Thanking You in advance. Pav

Re: [gmx-users] Pressure Question

Le 06/11/2014 06:16, Antonio Baptista a écrit : In particular, the virial-based "instantaneous pressure" (call it P') computed in simulations has its ensemble average equal to the thermodynamic pressure P (check any good book on molecular simulation). But, as others already pointed out, this

Re: [gmx-users] Version problem

Dear Satya, GMXRC is present in the installation directory. You need to find where you have installed the gromacs 5.0.2. Then locate the bin directory. GMXRC is generally present there. Chandan On Thu, Nov 6, 2014 at 2:00 PM, wrote: > Dear Dr. Carsten Kutzner, > I am unable to find the "

Re: [gmx-users] Version problem

Dear Dr. Carsten Kutzner, I am unable to find the "gmx5/bin/GMXRC" in my machine, used 'locate' and 'find' to search the location. However I have source the following: source /usr/share/gromacs/shell-specific/GMXRC.bashrc Without this also mdrun is running. I am definitely missing something.

Re: [gmx-users] Version problem

On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: > Dear all, > I am new to GROMACS, just finish installation of v5.0.2, started reading > online manual, as instructed executed the command: mdrun -version and the > printout pasted below. > > It is printing GROMACS version 4.6.5, howev