[gmx-users] CG

Hello. How could the martini CG-force-field could be used?You need to insert some input files or you can find somewhere this forcefield and "insert" it in the gromacs already excisted force-field list?Thank you!___ gmx-users mailing listgmx-users@g

Re: [gmx-users] installation problem

On Sun, 2009-02-01 at 23:34 -0300, Rafael Real Guerra wrote: > > > Hi > > Well, let’s start saying that I’m new at Linux and I’m trying to start > on Gromacs as well. > > I’ve been trying to install Gromacs 4.0 in my computer (laptop ACER > Aspire 4530, AMD Athlon 64X2) running Mandriva 2009

RE: [gmx-users] CG

well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html. From: doty_alex...@hotmail.comto: gmx-us...@gromacs.orgdate: Mon, 2 Feb 2009 10:09:03 +0200Subject: [gmx-users] CG Hello. How could the martini CG-force-field

Re: [gmx-users] Porcupine Plots

Hi Nahren, Gromacs does not include a tool for generation of porcupine plots. But if you're offered a means to do it through a webservice, all you really need is to take the extreme projections (two frames: g_anaeig -extr) and submit them. In a sense, you'll get the same thing if you load the extr

Re: [gmx-users] Porcupine Plots

Check the VMD list, you should find the script there. On Feb 1, 2009, at 9:28 PM, Mark Abraham wrote: nahren manuel wrote: Dear Gromacs Users, I have done PCA of my MD , I want to visually represent the motions in terms of porcupine plots. I came across Dynamite (web server) for this purpo

Re: [gmx-users] about dumping the last frame

Hi Shirin, The sed-solution is: sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}' traj.pdb Which might come in handy as an alias (csh-style:) alias lastmodel "sed -ne "/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}" -e "${x;p}" \!*' Hope it helps, Tsjerk On Mon, Feb 2, 2009 at 8:03 AM, nahren

RE: [gmx-users] infinite polymer crystals at gromacs 4.x.x

Hi, pbc=full is replaced by the mdp option periodic_molecules, which works both with pbc=xyz and pbc=xy. Berk > Date: Sun, 1 Feb 2009 17:45:13 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] infinite polymer crystals at gromacs 4.x.x > > Claus Valka wr

[gmx-users] how to get the original pdb file about CG DNA model

Hi all users, I am wondering how to get the original pdb file for CG DNA model. I have looked for this file in the website but no pdb file. Can anyone of you give me some suggestions how to get such file ? Thank you in advance. Yang ___ gmx-users ma

[gmx-users] Martini + other " force field "

Good afternoon, The reason of this email is to ask: is it possible to combine Martini's force field with the opls force field? The system is conformed by dopc membrane [Modeled by Martini's force field] with a small molecule of about 50 atoms [Modeled with opls. With all its hydrogens]. if th

Re: [gmx-users] how to get the original pdb file about CG DNA mode

Have you tried a web search? There are a number of sites that have databases of structures. Plus you could contact people that have published simulations using those molecules. What about the Protein Data Bank? Catch ya, Dallas Warren A polar bear is a Cartesian bear that has undergone a p

Re: [gmx-users] Martini + other " force field "

On Feb 2, 2009, at 10:19 PM, DAVID RINCON wrote: Good afternoon, The reason of this email is to ask: is it possible to combine Martini's force field with the opls force field? The system is conformed by dopc membrane [Modeled by Martini's force field] with a small molecule of about 50 a

Re: [gmx-users] energy groups

Hi, Justin I remove the del command. But I still got an error. make_ndx -f a.pdb -o a.ndx < make_ndx.input make_ndx.input: chain A and B& !a H* chain C& !a H* q checking input for internal consistency... Opening library file /export/apps/share/gromacs/top//ffG53a6.itp Opening library file /

Re: [gmx-users] energy groups

Alright, so how about the other comment I made? Are you using the right coordinate file? I recall you got this error when you used the non-pdb2gmx processed .pdb file as input into grompp. You must use the coordinate file that corresponds to your topology. -Justin Liu Shiyong wrote: Hi,

Re (in reply to Tsjerk): [gmx-users] Porcupine Plots

Dear Dr. Tsjerk, thanks for your reply. I got the clue from your reply and i did the same via VMD. But can you please be little more speicific about Pymol. I am not quite used to that software. regards, nahren --- On Mon, 2/2/09, Tsjerk Wassenaar wrote: From: Tsjerk Wassenaar Subject: Re: [

[gmx-users] protein crystallization

Hello, users. Can Gromacs do protein crystallization simulations? I tried looking for some information about it on mailings but failed. Would anyone give me some advice how to do it? Thanks. Best, william ___ gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] CG

doty alexiou wrote: well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html. It appears to be working now. As to your original question, I would say learn to walk before you run. I have used MARTINI only briefl

Re: [gmx-users] protein crystallization

Santan William wrote: Hello, users. Can Gromacs do protein crystallization simulations? I tried looking for some information about it on mailings but failed. Would anyone give me some advice how to do it? Thanks. Well, Gromacs can technically simulate galaxies, so I guess anything is poss

[gmx-users] free energy with TIP4P bug fixed

Hi Berk, Could you please post the relevant cvs diff here? While my energies are now output consistently for zero-step mdruns while separating my energygrps, I am still seeing some very aberrant behaviour when I apply the free-energy code during a 2-10 ns MD run, even with lambda=0.0. I get the

Re: [gmx-users] energy groups

pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6.minim_traj_withH_0.6.gro >r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1 Hi, Justin grompp read the co

Re: [gmx-users] energy groups

Liu Shiyong wrote: pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6.minim_traj_withH_0.6.gro >r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 2>&1

Re: Re (in reply to Tsjerk): [gmx-users] Porcupine Plots

Hi Nahren, If you're used to VMD and got what you wanted, why would you want to use Pymol for doing the same? Not that Pymol's not worth knowing :) In Pymol, check the help for the 'align' command: 'help align' Cheers, Tsjerk On Mon, Feb 2, 2009 at 11:51 AM, nahren manuel wrote: > Dear Dr. Tsj

Re: [gmx-users] energy groups

On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul wrote: > > > Liu Shiyong wrote: > >> >> >> >> pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p >> r-l_365130_G53a6.minim_traj_withH_0.6.top -i >> r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o >> r-l_365130_G53a6.minim_traj_

Re: [gmx-users] energy groups

Liu Shiyong wrote: Here is my command. pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb Why are you running pdb2gmx twice? Unless you have multiple proteins, and need multiple topologie

Re: [gmx-users] energy groups

command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx -f a.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr b.pdb ATOM 1 N ASP

[gmx-users] how to calculate the viscosity of the bulk

Hi, Justin: I saw in the manual that by g_energy -vis the viscosity of the system can be calculated. But when I perform the command i got this: @title "Bulk Viscosity" @xaxis label "Time (ps)" @yaxis label "\8h\4 (cp)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box

Re: [gmx-users] how to calculate the viscosity of the bulk

Yanmei Song wrote: Hi, Justin: I saw in the manual that by g_energy -vis the viscosity of the system can be calculated. But when I perform the command i got this: @title "Bulk Viscosity" @xaxis label "Time (ps)" @yaxis label "\8h\4 (cp)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @

Re: [gmx-users] energy groups

Alright, none of this looks like it will cause a problem. Can you post your em.mdp file? -Justin Liu Shiyong wrote: command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx -f

Re: [gmx-users] energy groups

Liu Shiyong wrote: command: + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb + editconf -f a6.gro -o a6.gro -d 20.0 + make_ndx -f a.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr I thi

Re: [gmx-users] Advice for simulating small DNA

On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote: No, I've no idea since I don't simulate DNA. In that case, thank you the help that much more! So I'm now attempting to add restraints for the base-pair H- bonds, but I'm having trouble. It seems like no matter what I try, my system reliably

Re: [gmx-users] energy groups

Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title = b cpp

Re: [gmx-users] energy groups

Liu Shiyong wrote: Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title

Re: [gmx-users] energy groups

Liu Shiyong wrote: Hi, Mark, I tried your suggestion. + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb + editconf -f a6.pdb -o a6.gro -d 20.0 + make_ndx -f a6.pdb -o a6.ndx + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr title =

Re: [gmx-users] Advice for simulating small DNA

Joshua Ballanco wrote: On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote: No, I've no idea since I don't simulate DNA. In that case, thank you the help that much more! So I'm now attempting to add restraints for the base-pair H-bonds, but I'm having trouble. It seems like no matter what I tr

[gmx-users] Re: IN4 molecule type error

Hi, I have added the #include "drg.itp" statement under the title, ; Include forcefield parameters in the .top file. Thr drg.itp is saved in the current directory. Still showing the sanme error as previous. including a part of the top file.Please check this. __

Re: [gmx-users] Re: IN4 molecule type error

Ms. Aswathy S wrote: Hi, I have added the #include "drg.itp" statement under the title, ; Include forcefield parameters in the .top file. Thr drg.itp is saved in the current directory. This is the incorrect order. You've inserted the drg.itp moleculetype information before your protein,

Re: [gmx-users] Re: IN4 molecule type error

Ms. Aswathy S wrote: Hi, I have added the #include "drg.itp" statement under the title, ; Include forcefield parameters in the .top file. Thr drg.itp is saved in the current directory. Still showing the sanme error as previous. including a part of the top file.Please check this. _

Re: [gmx-users] Re: IN4 molecule type error

Justin A. Lemkul wrote: Ms. Aswathy S wrote: Hi, I have added the #include "drg.itp" statement under the title, ; Include forcefield parameters in the .top file. Thr drg.itp is saved in the current directory. This is the incorrect order. You've inserted the drg.itp moleculetype inform