Re: [gmx-users] Re: the number of water molecules (Jian Zou)

Now, did you try searching the mailing lists before asking this? This question pops up once a week or so. Check the archives: the truth is out there. /Erik Dechang Li skrev: >> Message: 2 >> Date: Mon, 21 Apr 2008 10:43:27 -0400 >> From: "Jian Zou" <[EMAIL PROTECTED]> >> Subject: [gmx-users] Re:

[gmx-users] Re: ice box contact water box

Wei, Xiupeng wrote: Hi Mark, Could you give me some suggestions for how to put two boxes contacting each other? Thanks. Best regards, xiupeng Dear Vasilii and other users, Thanks for you reply. I triedto do the simulation you said. But how to setup the initial

Re: [gmx-users] water can't freeze

I think you'll have to do it manually. The geometry for ice shouldn't be too hard to find, and with that you can build your own coordinate file for a chunk of ice. Ice is not the only nucleating agent for water freezing though. In large scale nucleation protocols some silver compound is used if

Re: [gmx-users] Loop displacement calculation?

SeungPyo Hong wrote: Thank you for your kind response. I think that I do not clearly describe the system. The loop I mentioned above seems to interact with the other parts of the protein with hydrophobic interactions. So, the displacement of the loop from the original position will make the f

Re: [gmx-users] water can't freeze

There are several different crystal phases of water. For simulation setup, it's best (always, not only with freezing of water) to check the literature. This will also give you a hint on what have already been done. Quite a few MD simulations of ice were reported. If you have a good idea on what you

Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

On Mon, Apr 21, 2008 at 07:09:31PM +0400, Vasilii Artyukhov wrote: > Dear GROMACS users, > > particularly, those experienced with membrane simulations, > > I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain > small solutes, much like what was done in A.K. Sum & J.J. de Pabl

Re: [gmx-users] x2top error in CNT simulation

Hero wrote: Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT doub

[gmx-users] grompp error, invalid line in .gro file

Hello all. I'm trying to simulate an argon liquid. The OPLS-AA force field is used with the files from /usr/local/gromacs/share/gromacs/top. But I get an error when I run $ grompp -f NVT.mdp -c Ar.gro -p Ar.top --- Program grompp, VERSION 3.

Re: [gmx-users] grompp error, invalid line in .gro file

Just thinking out loud, but maybe "Argon" is too long of a name for the residues. The longest I think I've seen is 4 characters (something like LYSH or ARGN, for example). Maybe the length of the name is throwing off the formatting. Why don't you try again with a residue name of something like

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 67

set sel [atomselect $molid "selection"] for {set iframe 0} {$iframe < $nframe} {incr iframe} { $sel frame $iframe $sel update $sel get {the property you want} } you may go to vmd mailing list for more details. > Message: 1 > Date: Tue, 22 Apr 2008 10:42:56 +0800 > From: Dechang Li

Re: [gmx-users] grompp error, invalid line in .gro file

Justin A. Lemkul skrev: Just thinking out loud, but maybe "Argon" is too long of a name for the residues. The longest I think I've seen is 4 characters (something like LYSH or ARGN, for example). Maybe the length of the name is throwing off the formatting. Why don't you try again with a residu

RE: [gmx-users] grompp error, invalid line in .gro file

Hi, Your formatting is incorrect. The .gro format is a very old GROMOS fixed format (not free format). See the manual for the details: http://www.gromacs.org/documentation/reference/online/gro.html Berk. > Date: Tue, 22 Apr 2008 12:12:17 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.or

Re: [gmx-users] grompp error, invalid line in .gro file

Berk Hess wrote: Hi, Your formatting is incorrect. The .gro format is a very old GROMOS fixed format (not free format). See the manual for the details: http://www.gromacs.org/documentation/reference/online/gro.html Thanks for the link - I remember asking for it on this list years ago :-) I've

[gmx-users] Re: x2top error in CNT simulation (David van der Spoel)

Dear Gromacs, Actually, the error is for all the 144 atoms on SWNT_6_6_144: when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bonds Can not fi

Re: [gmx-users] Re: x2top error in CNT simulation (David van der Spoel)

Hero wrote: Dear Gromacs, Actually, the error is for all the 144 atoms on SWNT_6_6_144: when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bo

[gmx-users] genbox memory problem

Hello, I have a problem about genbox command in GMX. I'm running genbox to randamly insert molecules. Because the probobility of successful insertion is low, I have to use a large number for the "-try" variable. After running genbox I found sometimes the memory cost increased gradually after ea

[gmx-users] How to center my trimer in my simulation box.

Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thing in the center of my simulation cell but have failed miserably. I also search

Re: [gmx-users] How to center my trimer in my simulation box.

On Tue, 22 Apr 2008 14:14:19 -0700 "Ilya Chorny" <[EMAIL PROTECTED]> wrote: Hello, I am simulating a trimer in a membrane. In one of my simulation two of the monomers are on one side of the box and the other monomer is on the other side of the box. I tried using trjconv to center the whole thi

Re: [gmx-users] How to center my trimer in my simulation box.

Just to clarify. I would run trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? What would I run next? Thanks, Ilya On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Tue, 22 Apr 2008 14:14:19 -0700 > "Ilya Chorny" <[EMAIL PROTECTED]> wrote: > > > Hello, > > > >

Re: [gmx-users] How to center my trimer in my simulation box.

So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible? Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Ch

Re: [gmx-users] How to center my trimer in my simulation box.

I've often found it necessary to do multiple trjconv steps to get the result I want. So in this case, I'd probably make sure my protein is genuinely centered in the box, then take that output .xtc and then make sure everything is whole and approximately in the box (-pbc whole). - Original

Re: [gmx-users] Loop displacement calculation?

Thank you very much Mark~ On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > SeungPyo Hong wrote: > > > Thank you for your kind response. > > > > I think that I do not clearly describe the system. > > > > The loop I mentioned above seems to interact with the other parts of

[gmx-users] how to use GROMACS to model carbon nanotubes

I have put together this general response to the vast amounts of e-mails I have been receiving as of late in regards to how to use GROMACS to model carbon nanotubes. New GROMACS Users First if you are new to GROMACS step on before you even install the progr

Re: [gmx-users] How to center my trimer in my simulation box.

So I got it to work for my trimer by doing the following. 1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc 2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect The first step unwraps the whole trajectory and the second step wraps it back up. Cheers, Ilya -- Ilya Chorny Ph.D.

Re: [gmx-users] how to use GROMACS to model carbon nanotubes

> Additionally if some one would like to put this on GROMACS's wiki please > feel free to do so, I would but with graduation coming up I don't even > have > time to be writing this. If you would like the files I have on my site > those > can be provided for this purpose as well! Wikified here http

Re: [gmx-users] trjconv error

Hi, Sorry for not replying immediately. Gromacs ver 3.2.1 OS is Red hat enterprise 4 Initially I had tried reading the file from an external hard disk and now I copied it to another system and tried again. Still the same error. The reason why I was truncating was due to a magic number error I got

Re: [gmx-users] trjconv error

Ragothaman Yennamalli wrote: Hi, Sorry for not replying immediately. Gromacs ver 3.2.1 OS is Red hat enterprise 4 Initially I had tried reading the file from an external hard disk and now I copied it to another system and tried again. Still the same error. The reason why I was truncating was du