[gmx-users] g_covar with individual masses

Dear Gromacs users, I want to calculate the covariance matrix of the center of mass coordinates of non standard residues. Since I want to do it mass weighted I need to give the center of mass masses. From which file does g_covar read the masses? Thanks a lot Sebastian -- gmx-users mailing

Re: [gmx-users] Error when extending simulation

On 03/05/2013 03:50 PM, Mark Abraham wrote: ... and your GROMACS version! 4.6 running on nodes with NVIDIA Keppler K10 and Intel E5 CPU Mark On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul wrote: On 3/5/13 4:41 AM, sebastian wrote: On 03/04/2013 09:47 AM, sebastian wrote

Re: [gmx-users] Error when extending simulation

On 03/04/2013 09:47 AM, sebastian wrote: Hi Gromacs user, when I try to extend on of my simulations with mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt -append I get the following error Fatal error: Count mismatch for state entry disre_rm3tav, code count is 0

[gmx-users] Error when extending simulation

wrong. Any suggestion is very much appreciated Yours Sebastian -- 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 pos

Re: [gmx-users] Analysing of the trajectory using editconf

- -skip # takes only every #th frame. Best regards Sebastian On 29.01.2013 07:28, James Starlight wrote: Dear Gromac's users! I have long trajectory with small intervals between individual time-steps. Using editconf I'd like: 1- To extract last frame in pdb from my trajector

Re: [gmx-users] Re: gromacs 4.6 segfault

changes something Thanks Sebastian -- 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. Us

[gmx-users] gromacs 4.6 segfault

refcoord_scaling = all Pcoupltype = isotropic gen_vel = no gen_temp = 300 gen_seed = -1 Since I have no clue on which paramter should be tuned any guess would be very welcomed. Thanks Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] Gromacs 4.6 turn off ecc

Dear Gromacs user, is there a way to manually turn off ECC (gromacs version 4.6)? 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! * P

[gmx-users] gromacs 4.6 on NVIDIA K10

ction: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels How can I get mdrun working on the K10? Any hint is welcomed. Dears Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] strange lincs warning with version 4.6

buffer is automatically adjusted). -- Szilárd Mark On Tue, Dec 4, 2012 at 3:41 PM, sebastian< sebastian.wa...@physik.uni-freiburg.de> wrote: On 11/23/2012 08:29 PM, Szilárd Páll wrote: Hi, On Fri, Nov 23, 2012 at 9:40 AM, sebastian< sebastian.wa...@physik.uni-**fr

Re: [gmx-users] strange lincs warning with version 4.6

running on my local desktop with GPUs? As far as I know this is a rather typical set of parameters. The only difference what I can think of is that gromacs was compiled with intel and mkl libs on the cluster there as it was compiled with gcc and fftw3 libs on the local desktop. Sebastian Also

Re: [gmx-users] strange lincs warning with version 4.6

On 11/23/2012 08:29 PM, Szilárd Páll wrote: Hi, On Fri, Nov 23, 2012 at 9:40 AM, sebastian< sebastian.wa...@physik.uni-freiburg.de> wrote: Dear GROMCS user, I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my local desktop Watch out, the dirty version

[gmx-users] Installing 4.6 beta1

/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 I don't know what goes wrong and maybe I just miss a flag. Dears, Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Su

[gmx-users] strange lincs warning with version 4.6

coupl = no;berendsen tau_p = 0.1 compressibility = 4.5e-5 ref_p = 1.0 nstpcouple= 5 refcoord_scaling= all Pcoupltype = isotropic gen_vel = no;yes gen_temp= 300 gen_seed= -1 Thanks a lot Sebastian -

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

On 11/12/2012 04:12 PM, sebastian wrote: > Dear GROMACS user, > > I am running in major problems trying to use gromacs 4.6 on my desktop > with two GTX 670 GPU's and one i7 cpu. On the system I installed the > CUDA 4.2, running fine for many different test programs. > Compi

[gmx-users] Gromacs 4.6 segmentation fault with mdrun

going wrong any help is welcomed. Attached you find the log file. Thanks a lot Sebastian -- 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!

Fwd: Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2

Original Message Subject:Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2 Date: Mon, 29 Oct 2012 18:03:12 +0100 From: sebastian To: Jesper Sørensen Hi Jesper, thanks for the answer. It does not matter which card I choose. I was hopping that

[gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2

r: OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol The installed cuda version is 4.2 and the OpenMM version is 4.1.1 Since I have no idea whats going wrong any help is very welcomed Thanks a lot Sebastian -- gmx-users mailing list

Re: [gmx-users] g_helixorient

Hey, try xmgrace -nxy filename.xvg Best wishes Sebastian Am 21.11.2011 15:42, schrieb Poojari, Chetan: Hi, I have a peptide inserted in membrane would like to analyze the peptide tilt. The command i have used to do this is : g_helixorient -s .tpr -f .xtc -n .ndx -otilt Index file

Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'

Hey, thank you both for the response. I at least could restart the system. And it is running beyond the crashing point. Keep the fingers crossed. :) Kind regards Sebastian Am 12.08.2011 15:41, schrieb lina: On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers wrote: Dear all, searching

[gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'

rrors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Best regards Seba

[gmx-users] Re: multiple protein interaction

400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] multiple protein interaction > To: Discussion list for GROMACS users > Message-ID: <4e2ea759.30...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > smriti Sebastian wro

[gmx-users] multiple protein interaction

hi all, I am new to GROMACS.I would like to know how we will simulate putting more than two or more molecules of same proteins inside the box and do simulation?Is there any possibility to replace 100 atoms or so of solvent with proteins? Please help. Regards, smriti -- gmx-users mailing listg

[gmx-users] multiple molecule interaction

hi all, I am new to GROMACS.I would like to know how we will simulate putting more than two or more molecules of same proteins inside the box and do simulation?Is there any possibility to replace 100 atoms or so of solvent with proteins? Please help. Regards, smriti -- gmx-users mailing listg

Re: [gmx-users] Constraining two virtual sites

completely determined by the vsites, or am I wrong? Is there an easier solution? Thank you, Sebastian Hi, Unfortunately constraints can not be applied to virtual sites and grompp apparently does not not check for this. I will add a check. Constraints between virtual sites can lead to very complex

[gmx-users] Constraining two virtual sites

n). I am running the system with the sd integrator in (vers. 4.5.3) but also tried md and no thermostat, with no change in results. I appreciate any advice on this! Thanks, Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] DMSO compressibility

Hi all, can someone tell which compressibility should be used for DMSO at 300K? Thanks a lot Sebastian -- 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

Re: [gmx-users] g_covar & g_anaeig problems

Segmentation fault meaning it does not properly handle its memory. Nonetheless thanks again for the hydrogen advice. Had'nt really thought about it before. Kind regards Sebastian Am 07.09.2010 03:44, schrieb Mark Abraham: - Original Message - From: Sebastian Breuers Date: Tu

Re: [gmx-users] g_covar & g_anaeig problems

6368x46368) ... Reading frame 0 time0.000 Segmentation fault Meaning a matrix over around 46224x46224 elements starts to generate this problem. Did anyone encounter the same problem or does anyone has a hint to solve this issue? Kind regards Sebastian Am 25.03.2010 10:0

[gmx-users] different ref_t

I try to simulate a small peptide in CHCl3 there the peptide is couplet to a heat bath at a different temperature: tcoupl = nose-hoover tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.01 0.01 ref_t = 220 300 If I do so the temperature of the C

Re: [gmx-users] Re: Problem of reading the atom'force from trr file using template.c

Hi Chuan, in the template.c file is in the beginning the flag initialized: intflags = TRX_READ_X; If you want to read out the forces you have to change this to, as: intflags = TRX_READ_F; in addition to changing fr.x to fr.f. Basti On Wed, 23 Jun 2010 20:00:27 +0800 聂雪川 wr

[gmx-users] get the mass having the atom type

Hi all, I am using the template.c file to make some individual analyses. Using top.atoms.atomtype[i] I can get the information of the atom type of atom i. Is it then possible to use this information to get the mass of this specific atom? Thanks a lot -- gmx-users mailing listgmx-users@groma

Re: [gmx-users] constraints bond length vari by 10%

ke to know what does the shake_tol means. Thanks On Fri, 18 Jun 2010 09:37:36 +1000 Mark Abraham wrote: > > > - Original Message - > From: Sebastian Waltz > > Date: Thursday, June 17, 2010 18:59 > Subject: Re: [gmx-users] constraints bond length vari by >

Re: [gmx-users] constraints bond length vari by 10%

- Original Message - > From: Sebastian Waltz > > Date: Thursday, June 17, 2010 2:23 > Subject: Re: [gmx-users] constraints bond length vari by > 10% > To: Discussion list for GROMACS users > > > > Hi Mark, > > > > what I have written in the .to

Re: [gmx-users] constraints bond length vari by 10%

On Wed, 16 Jun 2010 09:05:20 +1000 Mark Abraham wrote: > > > - Original Message - > From: Sebastian Waltz > > Date: Tuesday, June 15, 2010 22:09 > Subject: [gmx-users] constraints bond length vari by 10% > To: gmx-users@gromacs.org > > > Hi all,

[gmx-users] constraints bond length vari by 10%

Hi all, I added constraints on some bonds in my system by adding [ constraints ] ;ai aj typedistance 40 41 1 0.1230 47 48 1 0.1230 54 55 1 0.1230 61 62 1 0.1230 to me top file (CO double bonds) and in the mdp file co

[gmx-users] pressure scaling more than 1%

Hi all, my simulation runs well for the first 70 steps with a step size of 0.001ps and when I get the warning that the pressure scaling is more than 1% every 1 step or so. So, is my tau_p of 0.2 to small or is the equillibration not done well enough. I am simulating a small peptide in CHCl

[gmx-users] which flag for the force

Hi all, I want to get the forces out of the .trr file using the template.c given. My question is what flag should I use in the last loop to get the force f? I don't find anything in the directory which is given in the example. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] Instantenous Hessian Matrix

Hi all, is there a way to get the hessian matrix for each time step for which I also print out the trr? Or do I have to run normal mode analysis for each configuration? Thanks a lot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] Forces on atom which is shifted out of the minimum

calculated? Does someone has any idea where to start? Thanks a lot Sebastian -- 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 req

[gmx-users] coinstraint bond length changes

(out of the .trr file). So I am not sure whats going wrong. This bonds are C O double bonds which have an equilibrium bond length of 0.143nm. Thanks a lot Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] g_anaeig -over: exact overlap definition?

-v2 has N eigenvectors, whereas -v2 contains only one eigenvector. (I found a way to do this.) Thanks, Sebastian -- 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&

[gmx-users] g_anaeig -over: exact overlap definition?

-v2 has N eigenvectors, whereas -v2 contains only one eigenvector. (I found a way to do this.) Thanks, Sebastian -- 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&

Re: [gmx-users] itp file

Hi, gunzip ccl4_box.tgz tar xvf ccl4_box.tar does work for me. Kind regards Sebastian anirban polley schrieb: Hi, I am surprise to see that not a single .tga ( e.g., ccl4_box.tgz <http://www.gromacs.org/@api/deki/files/32/=ccl4_box.tgz>) file can be open in the http://www.groma

Re: [gmx-users] Replica Exchange MD on more than 64 processors

Hey, thanks a lot for the quick answers. Installation of mvapich 1.2 and compiliation and linking of mdrun against their libraries seem to do the trick. Kind regards Sebastian Mark Abraham schrieb: - Original Message - From: Berk Hess Date: Wednesday, February 3, 2010 5:13

[gmx-users] Replica Exchange MD on more than 64 processors

if there is anyone else who is still facing the same problem or has already found a solution for this issue. Kind regards Sebastian -- _ Sebastian BreuersTel: +49-221-470-4108 EMail: breue...@u

[gmx-users] Replica Exchange MD on more than 64 processors

if there is anyone else who is still facing the same problem or has already found a solution for this issue. Kind regards Sebastian -- _ Sebastian BreuersTel: +49-221-470-4108 EMail: breue...@u

[gmx-users] Re: opls atom types and charges

ility of docked poses and for the calculation of binding free energies? simulations don't crash the way described in http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf - i only thought that oplsaa would probably be the 'better choice'? thanks for your estimation, sebastian

[gmx-users] opla atom types and charges for nitrile / thienopyridine

milar molecules, thanks in advance for any help! sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel: +49 (0)40 42838-3626 (-3484) mail: krug...@chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html -- gm

[gmx-users] Re: still problems with dodecahedron box and editconf

Hi Jochen, > trjconv -ur compact worked out very well, thanks! Sebastian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before post

[gmx-users] still problems with dodecahedron box and editconf

t part, but what about the 0 0 0 boxv ?!?   Maybe somebody can help me figuring out if my box is 'really' dodecahedron? Thanks in advance!   Sebastian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

Re: [gmx-users] multiple MD runs within ONE MD script

d of an MD run. Cheers, Sebastian David van der Spoel wrote: Sebastian Stolzenberg wrote: Hi everybody, (how) is it possible to write a single Gromacs MD script doing the following: 1.) Given a trajectory file (with say 100 frames), the MD script takes each of these 100 frames as initial

[gmx-users] multiple MD runs within ONE MD script

determines an average, and outputs the data into a seperate external file. I am mostly interested in point 1.) I know, there is a quick and dirty shell script way of doing this, but is it possible doing this also within one single Gromacs run? Thank you very much for your help, Regards, Sebastian