[gmx-users] Gromacs Topologies

Hi, I have updated the MKTOP script that was developed a few years ago. Now it can generate gromacs topology files for the forcefields amber03 and opls-aa. If anyone would like to use it, it can be found on www.aribeiro.net.br/mktop Cheers, Andre.-- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] problem with fullerene simulations

Oh sorry, i used spc.itp now and it works. Thanks. Srinivas. On Fri, Jul 22, 2011 at 5:48 PM, Justin A. Lemkul wrote: > > > jampani srinivas wrote: > >> Hi Justin, >> >> Thanks for your reply, i have no particular choice i was using it for my >> other work and just started with it. >> >> Now i

Re: [gmx-users] problem with fullerene simulations

jampani srinivas wrote: Hi Justin, Thanks for your reply, i have no particular choice i was using it for my other work and just started with it. Now i tried it again with spc model, I still get the following error. ++ Program grompp, VERSION 4.5.

Re: [gmx-users] problem with fullerene simulations

Hi Justin, Thanks for your reply, i have no particular choice i was using it for my other work and just started with it. Now i tried it again with spc model, I still get the following error. ++ Program grompp, VERSION 4.5.4 Source code file: toppush.c,

Re: [gmx-users] problem with fullerene simulations

jampani srinivas wrote: Hi Gromacs users, I am trying to run a fullerene simulaton in TIP4P water model, i am using the "c70_G53a6.itp " file downloaded from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model using genbo

[gmx-users] problem with fullerene simulations

Hi Gromacs users, I am trying to run a fullerene simulaton in TIP4P water model, i am using the "c70_G53a6.itp " file downloaded from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model using genbox command, later when i am tryin

[gmx-users] problems about number of frames in the edr file

Sorry, maybe I was not clear. Even before I do any eneconv on the edr file I mentioned, I could still only extract data of 4 frames though it seems there are around 2000 frames in it. Why is this happening? Zhuyi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] PS_PC system

Du Jiangfeng (BIOCH) wrote: Dear Gro-users, We made a PSPC(PS:20%, PC: 80%) membrane system. We want all the PS In one leaflet but every time after EM and MD, the PS lipids would scatter into both leaflets. Anyone knows how to keep PS in one leaflet? You haven't said you how prepared your mem

[gmx-users] PS_PC system

Dear Gro-users, We made a PSPC(PS:20%, PC: 80%) membrane system. We want all the PS In one leaflet but every time after EM and MD, the PS lipids would scatter into both leaflets. Anyone knows how to keep PS in one leaflet? Any suggestion is appreciated, Albert and Jiang. Jiangfeng Du, PhD

Re: [gmx-users] Simulation a labeled protein

Faezeh Nami wrote: For MD simulation of metalloproteins, people generally change the charge of atoms attached to the metal center based on quantum mechanics studies. If an .itf file shouldn’t be modified, how these changes can be made? QM studies will also tell you that fixed charges on me

Re: [gmx-users] Simulation a labeled protein

For MD simulation of metalloproteins, people generally change the charge of atoms attached to the metal center based on quantum mechanics studies. If an .itf file shouldn’t be modified, how these changes can be made? Faezeh On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul wrote: > > > Faezeh N

RE: [gmx-users] large error bars in PMF

I have used a cubic box of dimensions 8 x 8 x 14 (nm), and my total pulling was 5nm along the z direction. I dont´t think there could be a problem with the PBC, since the layer of solvent around the protein is quite big, although I suppose that using a dodecahedron box for this system would hav

Re: [gmx-users] Residence time and trjorder

Carla, The g_residence.c is written in accord to gmx-4.5.4 format. What you can do is copy it to the src/tools directory. Make a subsequent changes in the Makefile present there and the do make to compile. This will generate g_residence executable, which can be used. But I did not understand, how

[gmx-users] large error bars in PMF

I see now what you mean. As it happens, I doubt that this would have caused the problem since no force was applied on X and Y dimensions, so it would require that there was a PBC-based distance degeneracy along Z, although this is of course possible and hopefully Rebecca will answer this pa

Re: [gmx-users] Simulation a labeled protein

Faezeh Nami wrote: Dear Itamar Thank you for the reply. If I modify Cys parameters in the *rtp file in order to add the Cys-label parameters, it will be applied to other Cys in the protein as well. Isn't it? Set the name of your modified residue to something unique (in both the input c

Re: [gmx-users] large error bars in PMF

chris.ne...@utoronto.ca wrote: I don't see why the box-type makes any difference whatsoever. It is possible that if you use a rhombic dodecahedron, you may reduce the system size, thus simulate more ns/day, thus converge faster, but that should be the only effect. I would be interested to hea

Re: [gmx-users] Simulation a labeled protein

Dear Itamar Thank you for the reply. If I modify Cys parameters in the *rtp file in order to add the Cys-label parameters, it will be applied to other Cys in the protein as well. Isn't it? In case of modification of *itp file, should I modify all nr or qtot after the Cys? What about bonds? Best

[gmx-users] large error bars in PMF

I don't see why the box-type makes any difference whatsoever. It is possible that if you use a rhombic dodecahedron, you may reduce the system size, thus simulate more ns/day, thus converge faster, but that should be the only effect. I would be interested to hear more from Justin about how

Re: [gmx-users] Residence time and trjorder

Hi Baofu, Please can you tell me how to install g_residence.c in gromacs? If I understood well, the line command is the following: g_residence -s toplogy.tpr -f trajectory.xtc -o output What is the format of the output? Thank you, Carla On Tue, Jul 12, 2011 at 2:32 PM, Baofu Qiao wrote: > H

RE: [gmx-users] large error bars in PMF

Forget my last mail, I was not seeing the box correctly. Sorry about that. Best wishes, Rebeca. From: rega...@hotmail.com To: jalem...@vt.edu; gmx-users@gromacs.org Subject: RE: [gmx-users] large error bars in PMF Date: Fri, 22 Jul 2011 10:15:27 + CC: Hi again, I have one doub about

[gmx-users] g_bundle -na option for calculating angle between helices

Hi I am trying to calculate angle between helices using g_bundle and: http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html I am unable to understand how the -na option works. "the program reads 2 index groups

RE: [gmx-users] large error bars in PMF

Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron? Thanks a lot for your help. Be

[gmx-users] R: R: Re: g_cluster error in rhombic dodecahedric system

Dear Tsjerk, once again thank you for your very useful suggestions. I'm not sure that there are many clusters in my trajectory, so I don't want to lower my cutoff. Instead I'm quite surprise to find that it should be a problem related to the absence of transitions, I don't understand why the progra