[gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat

Dear Gromacs users, I have been trying to use the recolor.sh mentioned in this wbsite http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html to reclor an xpm file called rmsd-matrix.xpm file, whenever I issue the command recolor

Re: [gmx-users] NMA

Yao Yao wrote: HI Gmxers, Anyone came across a step-by-step tutorial for normal mode analysis, not a theoretical background introduction but a practical hands-on demonstration in gromacs? I dunno what steps to follow. http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis -Justi

[gmx-users] NMA

HI Gmxers, Anyone came across a step-by-step tutorial for normal mode analysis, not a theoretical background introduction but a practical hands-on demonstration in gromacs? I dunno what steps to follow. Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] Com Pulling

I understand your intention now. It might be possible to do this with gromacs 3.3.3 (short pull code simulation, then restart without the pull code but using the .trr from the previous run) but I'm not sure if you can do that with 4.x. Note that a thermostat is going to remove this directed

[gmx-users] Re: RE:Com Pulling

Dear Chris Neale, I wanted to generate directed initial velocities for two seperate multiprotein complexes, but just so they start to move through the void towards each other. The only way I found to do this was to use the COM pulling, but then it is a "biasing" force applied across the entir

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hello, This is the output from deviceQuery command: ./deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) There are 4 devices supporting CUDA Device 0: "Tesla T10 Processor" CUDA Driver Version: 3.20 CUDA Runtime Version:

Re: [gmx-users] How to define Center of Mass velocity of a specific group

Tomy van Batis wrote: On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul > wrote: Tomy van Batis wrote: Dear all I have a system consisting of 2 substrates (20 nm distance between them) and inside them there are polymer chains. I would

[gmx-users] pullx.xvg / pullf.xvg

please copy and paste your commands your output. It is unlikely that any of us are going to do that tutorial in order to understand your question. -- original message -- Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella

[gmx-users] Com Pulling

If I understand correctly, you want to apply a biasing force and you also want to have an "unbiased" simulation. These two things are not possible in combination. There are a variety of techniques available that will give you particular information. For example, you can extract the unbiased

Re: [gmx-users] Question about Extention simulation in REMD

Qin Qiao wrote: Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi p

Re: [gmx-users] RE: Log files

Nimesh Jain wrote: How do I turn off md.log fine generation in Gromacs? You can probably just set nstlog = 0 in the .mdp file. -Justin Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemis

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Bongkeun Kim wrote: Hello, I tried using 1fs timestep and it did not work. I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not supported gpu and I had to use "force-device=y". Do you think this is the reason of the error? Probably. Please note the documentation and the s

[gmx-users] Re: Com Pulling

Dear All, I was setting up things to use COM pulling for a multiprotein complex. My question after going through the gromacs documentation(online) is: Is there a way to limit either the time or distance two groups are pulled towards each other(reguarding only the applied force), as I could not

Re: [gmx-users] RE: Log files

I don't think you can turn out log file generation (note that it's not an optional output). If you don't want to write intermediate steps in this file you can set: nstlog = 0 in your mdp file. In any case, the first and last step will be written. Javier El 15/12/10 16:20, Nimesh Jain escri

Re: [gmx-users] How to define Center of Mass velocity of a specific group

On Tue, Dec 14, 2010 at 2:19 PM, Justin A. Lemkul wrote: > > > Tomy van Batis wrote: > >> Dear all >> >> I have a system consisting of 2 substrates (20 nm distance between them) >> and inside them there are polymer chains. I would like during my NVT >> simulations the substrates NOT to move (I su

[gmx-users] RE: Log files

How do I turn off md.log fine generation in Gromacs? 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! Please don't post (un)subscribe requ

[gmx-users] pullx.xvg / pullf.xvg

Hi, I am following the umbrella sampling tutorial written by Justin Lemkul. I was successfully able to run the umbrella sampling simulations, but for each configuration it outputted a single xvg file. For the data analysis i should have pullf.xvg / pullx.xvg filesbut these files are not ou

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hi, Tesla C1060 and S1070 should is definitely supported so it's strange that you get that warning. The only thing I can think of is that for some reason the CUDA runtime reports the name of the GPUS other than C1060/S1070. Could you please run the deviceQuery from the SDK and provide the output h

[gmx-users] g_rotacf NH vector relaxation

Dear gromacs users, I want to calculate NH vector for my ligand simulations using g_rotacf. I want to ask if I first need to remove rotation and translation degrees of freedom from the trajectory using the command: trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc Also, wh

[gmx-users] Question about Extention simulation in REMD

Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I guess it

Antw: Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hello Did you use constraints = none instead of LINCS. It could work better bests, Emanuel >>> Bongkeun Kim 15.12.10 9.42 Uhr >>> Hello, I tried using 1fs timestep and it did not work. I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not supported gpu and I had to use "

RE: [gmx-users] pathologically expanding box

Hi, I think the problem is epsilon_r=80, which reduces your electrostatics interactions by a factor of 80. Berk > Date: Mon, 13 Dec 2010 17:46:14 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] pathologically expanding box > > > > Greg Bowman wrote: > >

Re: Antw: [gmx-users] NaN error using mdrun-gpu

Hello, I tried using 1fs timestep and it did not work. I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not supported gpu and I had to use "force-device=y". Do you think this is the reason of the error? Thanks. Bongkeun Kim Quoting Emanuel Peter : Hello, If you use for y

Antw: [gmx-users] NaN error using mdrun-gpu

Hello, If you use for your timestep 1fs instead of 2fs, it could run better. Bests, Emanuel >>> Bongkeun Kim 15.12.10 8.36 Uhr >>> Hello, I got an error log when I used gromacs-gpu on npt simulation. The error is like: --- Inp