Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 134, Issue 45

Hi everyone I'm going to run md simulation but when i use grompp command i face this warning: WARNING 1 [file "DRGGMX.ITP", line 18]: >Too few parameters on line (source file toppush.c, line 731) can everyone help me please? On Mon, Jun 8, 2015 at 2:18 PM, < gromacs.org_gmx-users-requ...@m

[gmx-users] Hi

I am going to run md but when i use grompp command i face this warning: WARNING 1 [file "DRGGMX.ITP", line 18]: >Too few parameters on line (source file toppush.c, line 731) can everyone help me please? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Su

Re: [gmx-users] which file to use to analyze trajectory using code

Thanks for the link Eric ! I am unable to open the following link though - ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz On Tue, Jun 9, 2015 at 9:31 AM, Eric Smoll wrote: > Hello Sahithya, > > Here is one solution: > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

Re: [gmx-users] download problem

Dear Justin,I'm having a hard time. So please help me.I was using Gromacs 5.0.4 where I encountered this bug regarding g_x2top. So I removed 5.0.4 to replace it with another version. But now I find all download links broken, and I really need to proceed with my project and I'm too short of time.

Re: [gmx-users] which file to use to analyze trajectory using code

Hello Sahithya, Here is one solution: http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library Best, Eric On Mon, Jun 8, 2015 at 9:56 PM, Sahithya S Iyer wrote: > Dear users, > > If one wanted to analyze the trajectory obtained on production run for a > property of the protein that

[gmx-users] which file to use to analyze trajectory using code

Dear users, If one wanted to analyze the trajectory obtained on production run for a property of the protein that is not already defined in the gromacs programs, which file should be used for analysis ? If one were to write an external code to analyze this property, .trr, .tpr, .xtc files cannot

Re: [gmx-users] Atomtype OW not found

Hi Rasha, I suspect your difficulties might be caused by the way you are converting the parameters. You may have more luck using acpype to convert your GLYCAM carbohydrate topologies into Gromacs formatted ones. Once you obtain your ligand coordinate and paramet

[gmx-users] Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins

Immediate PhD Opening In Dr. Khaled Barakat’s Lab, Faculty OfPharmacy, University Of Alberta.   Specialization: Computational Structural Biology Of MembraneProteins   Term: 4 Years Fully Funded PhD Studentship   A four years fully funded PhD studentship is available immediatelyin the comput

Re: [gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb

Additional info: The base system is a SuperMicro X8DTG-D motherboard with dual Xeon E5620 CPUs at 2.4 GHz, and 24 GB of DDR3 ECC RAM The GPUs are two NVidia Tesla C2075s Running under Ubuntu 14.04 LTS 64-bit, kernel 3.13.0-53, with CUDA 7.0, installed via the NVIDIA-provided .deb file, cuda-repo

[gmx-users] cudaStreamSynchronize failed in cu_blockwait_nb

Hi all, I am running a GPU-accelerated test (GMX 5.0.5) and, after about 60K steps of what seems to be a huge speed-up, I get the error from the subject with the following comment: "unspecified launch failure." This is on an 8-core (16-thread) Intel CPU and two Tesla cards. The run command is: m

[gmx-users] gmx distance

Helecho "3 4"| g_distlo, i want to introduce a coomand in Gromacs 5.0.4 with the initial echo "3 4"| g_dist. Should i use gmx distance echo "3 4"| g_dist and the rest of the commnand? This is the complete command i want to use echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc -s dppc128_1.tpr -o

Re: [gmx-users] Microwave

Dear Mark, The authors didn't circulate the modified version of GROMACS and they couldn't be able for any help. It would be very kind of you if you could give me some information about which file or files of the source code should I alter for achieving this purpose. Best, Mostafa On Mon, Jun 8,

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

More details are available on the plumed forum google group at https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ > Hi, > > I have successfully installed plumed-2.1.2 (I believe with MPI > capabilities) and patched it onto gromacs-5.0.4,

Re: [gmx-users] OPLS definition of Phenyl palmitate

Maybe this is of interest to others so I will write what I did. I built a phenyl acetate and methyl acetate: O_2 || CA - CA C_2 / \ / \ CACA - OSCT \

Re: [gmx-users] Error

NaN means "not a number" and usually it means some force went to infinity and thus your system is exploding. running on a larger cluster won't be of any help, you have to move one step back and perform a proper energy minimization. if the error persists, you should also check your topology for any

Re: [gmx-users] Error

Dear Andre sir, Thank you for your reply. I have gone through the threads but I didn't got the exact solution for my problem. I have run the protein-ligand system upto nvt.tpr mdrun execution steps in my laptop with Ubuntu. It is running comfortably but showing the output -nan. Therefore, I tho

Re: [gmx-users] SwissParam itp files

Hi Justin and Albert Thanks for your help. In order to reply Justin's comment I would like to say that there are numerous examples of such kinds of fullerene-organic binder interaction. http://www.sciencedirect.com/science/article/pii/S0045653513001215# If you look at the above paper, t deals wi

[gmx-users] Syntax to use "gmx convert-tpr"

Dear GROMACS experts, Can I ask if the following commandlines are correct for extending simulations? gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append (My job.sh can be found at https://copy.com/lrFubrlq9

Re: [gmx-users] SwissParam itp files

It's not accurate enough. you'd better use Cgen FF from Gromacs. On 06/08/2015 12:33 PM, soumadwip ghosh wrote: Dear users, I am trying to see the interaction between fullerene and water soluble binders using GROMACS 4.5.6 and CHARMM 27 all atom force field. I made the topo

Re: [gmx-users] All bulk is moving during Umbrella sampling

Justin, thank you for the advice. But if I apply a force to keep molecules within a layer, how I will extract this force effect on PMF? On Sun, Jun 7, 2015 at 3:59 PM, Justin Lemkul wrote: > > > On 6/6/15 2:57 PM, gozde ergin wrote: > >> Actually I know I need to do something like this however

Re: [gmx-users] Pressure Coupling in GROMACS

Thanks for your reply Dr. Lemkul. I came across some of the widely fluctuating pressures before but the average pressure was more or less close to the target values previously (even though the instantaneous values varied quite a lot). But in my case, the average pressure is far different from the

Re: [gmx-users] OPLS definition of Phenyl palmitate

Thanks for your response. First of all I must say it is a bit strange that OPLS has the atom types of phenyl ester but not the corresponding dihedral angels to support it. But I see your point but could you elaborate on how I could evaluate this? How can I calculate those profiles? Thanks, Max

Re: [gmx-users] Extending simulation not work: always re-start from the beginning

On 6/8/15 9:19 AM, Zhang, Cheng wrote: Dear Gromacs expert, I was trying to extend my simulations. Relevant files can be found at https://copy.com/c8dDMnC0df2gbig9 To prepare the "md_0_1.tpr" file, I set the following in the "md_50ns.mdp" so that it can run 50 ns in total. nsteps = 25000

Re: [gmx-users] Pressure Coupling in GROMACS

On 6/8/15 9:10 AM, Jashimuddin Ashraf wrote: Dear GROMACS users, I am new to GROMACS. My system contains only carbon nanotubes and inside my md.mdp file I have- . . Pco

Re: [gmx-users] Pressure Coupling in GROMACS

Hi Ashraf, from the gromacs website (http://www.gromacs.org/Documentation/Terminology/Berendsen): The distribution of temperatures and pressures (in the case of the thermostat and barostat, respectively) does not correspond to any known statistical mechanical ensemble. It is best applied duri

Re: [gmx-users] download problem

On 6/8/15 8:30 AM, Nima Sa wrote: Hi, Dear users,When I click to download a gromacs.tar.gz file from www.gromacs.org/Downloads, the download does not start and it says the webpage is not available. Do you know what the problem is? Can anyone download any item? for example, gromacs-5.0.5.tar

[gmx-users] Extending simulation not work: always re-start from the beginning

Dear Gromacs expert, I was trying to extend my simulations. Relevant files can be found at https://copy.com/c8dDMnC0df2gbig9 To prepare the "md_0_1.tpr" file, I set the following in the "md_50ns.mdp" so that it can run 50 ns in total. nsteps = 2500 dt= 0.002 Then I submit the same

[gmx-users] Pressure Coupling in GROMACS

Dear GROMACS users, I am new to GROMACS. My system contains only carbon nanotubes and inside my md.mdp file I have- . . Pcoupl = berendsen Pcoupltype

Re: [gmx-users] download problem

Hi, Dear users,When I click to download a gromacs.tar.gz file from   www.gromacs.org/Downloads, the download does not start and it says the webpage is not available. Do you know what the problem is? Can anyone download any item? for example, gromacs-5.0.5.tar.gz..Thanks in advance.  On Mon

Re: [gmx-users] SwissParam itp files

On 6/8/15 6:33 AM, soumadwip ghosh wrote: Dear users, I am trying to see the interaction between fullerene and water soluble binders using GROMACS 4.5.6 and CHARMM 27 all atom force field. I made the topology by SwissParam web server for both fullerene and the organic binder

[gmx-users] SwissParam itp files

Dear users, I am trying to see the interaction between fullerene and water soluble binders using GROMACS 4.5.6 and CHARMM 27 all atom force field. I made the topology by SwissParam web server for both fullerene and the organic binder and my topology file looks like this- GROMACS

[gmx-users] download problem

Hi,I'm trying to download a gromacs.tar.gz file from www.gromacs.org/Downloads  but most of the links seems to be broken.Does anyone know what the problem is?Thanks  -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before p