[gmx-users] Non Equilibrium MD

Apoorv, I have two questions regarding non equilibrium MD simulations in GROMACS. 1) If we use a thermostat (with T=300 K), will it subtract the non zero streaming velocity to maintain the temperature or will it reset the total velocity. Different thermostats work differently. Read the equatio

[gmx-users] problem in executing genbox command

Hi all , Whenever i am running the genbox command I am getting the following error :- genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top :-) G R O M A C S (-: Segmentation fault (core dumped) Can anybody tell me whats the reason for such

[gmx-users] questions about umbrella sampling

Dear R-X Gu, I think that you didn't get a reply because you are clearly using gromacs version 3.x and many of us now work with gromacs 4.x. (Note that the .ppa file is gone in gromacs version 4.x and the pull parameters now go into the regular .mdp file). If there is some reason that you

Re: [gmx-users] ./mdrun-gpu fatal error

lin hen wrote: Yeah, I think my problem is the input, but I don't have the .mpd file, I am using the existing input which has no problem with Gromacs 4.0.5 using ./mdrun-openmm. So is there any other way I could modify? No. You need to generate a sensible input file. -Justin Thanks,

RE: [gmx-users] ./mdrun-gpu fatal error

Yeah, I think my problem is the input, but I don't have the .mpd file, I am using the existing input which has no problem with Gromacs 4.0.5 using ./mdrun-openmm. So is there any other way I could modify? Thanks, YY > Date: Fri, 5 Nov 2010 19:54:10 -0400 > From: jalem...@vt.edu > To: gmx-

Re: [gmx-users] ./mdrun-gpu fatal error

lin hen wrote: Thanks a lot for your reply, I didn't have this .mdp file, and I attached the log file, how to modify? You don't have an .mdp file? Then how did you create your input .tpr file? This is the only way to fix your problem - specify proper input parameters in the .mdp file.

Re: [gmx-users] ./mdrun-gpu fatal error

lin hen wrote: Hi, I am new for gromacs, I am trying to run the mdrun-gpu executable: the step to build the mdrun-gpu: 1. disable the shared libraries: //disable shared libraries (can be problematic with MPI, Windows) BUILD_SHARED_LIBS:BOOL=OFF 2. export LD_LIBRARY_PATH=/path to o

[gmx-users] ./mdrun-gpu fatal error

Hi, I am new for gromacs, I am trying to run the mdrun-gpu executable: the step to build the mdrun-gpu: 1. disable the shared libraries: //disable shared libraries (can be problematic with MPI, Windows) BUILD_SHARED_LIBS:BOOL=OFF 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/li

Re: [gmx-users] elastin

mustafa bilsel wrote: Hi all, I would like to simulate (VPGVG)18, but it is pdb isn't in protein data bank. Where can I find it? OR How can I simulate it under this condition? http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Best wishes -- ===

[gmx-users] elastin

Hi all, I would like to simulate (VPGVG)18, but it is pdb isn't in protein data bank. Where can I find it? OR How can I simulate it under this condition? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

She uses "trjconv -pbc atom", so it looks like the answer is no. On Fri, Nov 5, 2010 at 6:10 PM, Tsjerk Wassenaar wrote: > Hey, > > Do the holes match the parts of the protein sticking out on the other side? > > Tsjerk > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

Hey, Do the holes match the parts of the protein sticking out on the other side? Tsjerk On Nov 5, 2010 8:14 PM, "Vitaly Chaban" wrote: On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz wrote: > hi vitaly, > > the only acetonitrile boxe that i was able to find is the one provided by > christoph fre

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz wrote: > hi vitaly, > > the only acetonitrile boxe that i was able to find is the one provided by > christoph freudenberger in 2003: > > http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz Maybe somewhere on other old website if they lost it while

[gmx-users] Re: genbox generating acetonitrile box with holes

Diana - I just wonder how the density of your system behaves while you run NPT equilibration? Do you monitor it? Did you estimate the size of these holes? Maybe they are just due to a visualization utility that uses inappropriate atomic radii? Vitaly On Fri, Nov 5, 2010 at 2:05 PM, dlousa wro

[gmx-users] Re: genbox generating acetonitrile box with holes

Hey, Diana - I believe these acetonitrile holes are not a problem. Just perform an equilibration run in the NPT ensemble and they will disappear. The more tricky way is to adjust VDW radii in vdwradii.dat before using genbox. By the way, what force field model of acetonitrile do you use here? Som

Re: [gmx-users] g_cluster: optimal cutoff

Hi, I am also trying to do clustering analysis, but g_cluster version 4.5.1 seems to have a bug. it does not crash but show strange std output like # RMSD calculations left: -897758633 and the stopps after some time. Which version do you guys use? Best, Xiaohu On 11/05/2010 06:57 AM, Fab

Re: [gmx-users] continue Prod run from NPT eq

manu.mura wrote: Dear Justin, I run again the simulation, this time I keep the same thermostat (Nose-Hoover). I still get the same error manu.mura wrote: READ 3 BOX VELOCITIES FROM final_NPT.edr --

[gmx-users] continue Prod run from NPT eq

Dear Justin, I run again the simulation, this time I keep the same thermostat (Nose-Hoover). I still get the same error manu.mura wrote: READ 3 BOX VELOCITIES FROM final_NPT.edr --- P

Re: [gmx-users] genbox generating acetonitrile box with holes

On 6/11/2010 12:54 AM, Diana Lousa wrote: Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying

Re: [gmx-users] genbox generating acetonitrile box with holes

Diana Lousa wrote: Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying to solvate a protei

Re: [gmx-users] dssp

On 6/11/2010 12:57 AM, #ZHAO LINA# wrote: Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) People who might spend their time to give free help are not at all interested in things th

RE: [gmx-users] dssp

Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf o

Re: [gmx-users] dssp

#ZHAO LINA# wrote: But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.

[gmx-users] genbox generating acetonitrile box with holes

Dear all, I tried to send this message earlier, but I had attached a pdb file and apparently it exceeded the size allowed in the mailing list and is awinting for the list moderator to evaluate it. I apologize if the message is sent twice. I am trying to solvate a protein in a box of acetonitrile u

RE: [gmx-users] dssp

But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal err

RE: [gmx-users] dssp

Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the "real and true" path to a simple way as it showed "pathTo..." before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, l

RE: [gmx-users] dssp

I did choose 1 protein when it asked me to choose. Thanks for your answering, I may try on my desktop another time. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Linus Östberg [bio...@talavis.eu] Sent: Friday, Novem

Re: [gmx-users] dssp

Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be un

Re: [gmx-users] dssp

What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# wrote: > Hi, > > Thanks for your response, I modified that

RE: [gmx-users] dssp

Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina

Re: [gmx-users] installation of gromacs on windows using cygwin

bharat gupta wrote: I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the fol

Re: [gmx-users] dssp

#ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null 2> /dev/null It came out two or three file like ddEPI6I2 and then died l

[gmx-users] dssp

Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null 2> /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first tim

Re: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2

Hi, all this has now been fixed I hope. The residues that I had missed are the ones my scripts not directly parse from the CHARMM ff files, i.e. they are hardcoded and hence I forgot to update the charge groups on them. Berk has now added an option of -1 to atoms added to terminals so that they

Re: [gmx-users] installation of gromacs on windows using cygwin

I think I was installing the linux version of fftw3 on windows .. I downloaded this file - fftw-3.2.2.pl1-dll32.zip for installation .. but ./configure command is not working for this file ... as I am getting the following error $ ./configure

Re: [gmx-users] installation of gromacs on windows using cygwin

I followed the same instructions given in the gromacs manual , step by step ... I first tried installing gromacs with the first command given in the manual and then again I installed with the options for FLAGS but finally ended up with the following error in both the above mentioned conditions :-

Re: [gmx-users] Targeted Energy Minimization

On 5/11/2010 4:53 PM, Yao Yao wrote: Hi Gmxers, Is that possible that in mdp file, only a specifically-targeted part inside/of the protein is energy minimized (EM)? Like, just wanna EM the ligand or one out of the two proteins in protein-docking. I'm not sure, but freeze groups + EM might

Re: [gmx-users] installation of gromacs on windows using cygwin

On 5/11/2010 6:30 PM, bharat gupta wrote: Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be locat

Re: [gmx-users] g_cluster: optimal cutoff

On 10/31/2010 08:20 PM, Valeria Losasso wrote: > Dear all, > for my cluster analysis I am using the g_cluster tool with the gromos method. > The problem is that I have to compare the results for system of different > lengths, and of course the result of the cluster analysis changes according > to

Re: [gmx-users] which force file has parameters for creatine md simulations

#ZHAO LINA# wrote: http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta The usual caveat applies: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips The raw output of PRODRG is often quite unsatisfactory and inconsistent with any Gromos96 parameter set. -Justin lina --

[gmx-users] which force file has parameters for creatine md simulations?

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef

RE: [gmx-users] which force file has parameters for creatine md simulations

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Olga Ivchenko [olga.ivche...@gmail.com] Sent: Friday, November 05, 2010 6:02 PM To: gmx-users@gromacs.org Subject: [gmx-user

[gmx-users] which force file has parameters for creatine md simulations?

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef

[gmx-users] which force file has parameters for creatine md simulations

Dear All, I want to do molecular dynamics with creatine. But I can not transform creatine pdb file downloaded from drugbank to gromac topology file using command: pdb2gmx -f Please can you write me if there is a force filed for which creatine parameters are already exist and I can use this forcef

Re: [gmx-users] installation of gromacs on windows using cygwin

Hi, If you have installed fftw3 in the standard location it whould work out of the box. Otherwise, you have to set the LDFLAGS and CPPFLAGS to the library and include location respectively. However, there's one more thing I can think of: did you make sure that you compiled fftw3 in single precisi

[gmx-users] installation of gromacs on windows using cygwin

Hi there .. I have been trying to install gromacs on windows using cygwin .. and after the installation of the fftw3 package , the moment i install the gromacs using the first command ./configure .. It gives an error that fftw3 package cannot be located .. can anybody pls help find out where am I