Re: [gmx-users] periodic boundary condition

Dear David, I tried to use x2top, but it ended up with the following error: 0: GROMOS96 43a1 force field  1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 2

[gmx-users] single and double

My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p waters. Prior to adding counterions, grompp yields a net charge of -1.73 and grompp_d yields -2.0. Once I have added counterions, both single and double precision don't give me a warning about a net charge on the

Re: [gmx-users] Re: The molecule size (jiqing)

主月 ：） wrote: > Hi: > Two things, > > - maybe you need a larger systems > - maybe g_gyrate does not take periodicity into account correctly. > extract some single molecules and look at them in a viewer, or write > your own script to compute Rg. > - have you used pbc = full for the simulations? >

[gmx-users] Re: The molecule size (jiqing)

Hi:>  > >  > Two melt models were built for polyethylene (PE) and>  > polyvinylmethylether (PVME) melt with PBC condition .>  > >  > The density of both melt model agree with experimenal value well.But>  > when one check the radius of gyration (Rg) of them, both of them were>  > too

Re: [gmx-users] single point calculation

Reynier Suardiaz del Río wrote: Hi, is my firt question in the list, i have a very simple and posibly a very nonsense question. do i have to use mdrun to performe a single point calculation of a certain conformation? how? is there something to specify in .mdp file? Just do a zero step minimi

Re: [gmx-users] Gromacs install question

Qiao Baofu wrote: Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory o

Re: [gmx-users] velocities

Prasad Gajula wrote: Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random nu

[gmx-users] job opportunity

I am writing to call this community's attention to the job opportunity at http://www.nanoconductor.org/jobs/NCN_at_UIUC_Lead_Scientist.pdf which would involve Gromacs expertise in addition to other software relevant to nanoscience. Thanks for your attention, Eric --

回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p

Thank you for your advise!raja <[EMAIL PROTECTED]> 写道： HI Zhao,To compute RMSIP, you have to compute eigenvector using gromacs utilityprogram then from that trajectory you can compute RMSIP using a scriptwhich I got from Tsjerk Wassenaar from this list. You can appraoch him.Regards,B.NatarajOn Mon

回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p

Dear Tsjerk : Thank you very much!Tsjerk Wassenaar <[EMAIL PROTECTED]> 写道： Hi Xi Zhao,Please find attached a .csh script you can use to calculate the rmsip.The script is of the hand of Isabella Daidone, now in Heidelberg.Note that for a set of 'equal' simulations there is a spread in thevalues yo

回复： RE: [gmx-users] r.m.s.i.p

how to use it in detail?Thanks!"Fan, Fenghui " <[EMAIL PROTECTED]> 写道： Try RMSD fit function.-Original Message-From: [EMAIL PROTECTED] on behalf of xi zhaoSent: Mon 9/18/2006 2:12 AMTo: gmx-users@gromacs.orgSubject: [gmx-users] r.m.s.i.pDear Gromacs users:I am a new gromacs user, I want ro

RE: [gmx-users] Gromacs install question

In your sudirectory of the newly established Gromacs directory, there will subdirectory tools and kernel. You can start your commands in these subdirectory and it should work. Best regards. Fenghui Fan -Original Message- From: [EMAIL PROTECTED] on behalf of Qiao Baofu Sent: Mon 9/18/

[gmx-users] velocities

Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200

[gmx-users] bonds

Hi! I have a question . I am working with a protein that they will count twocenters FES co-ordinated for cisteins, these cisteins were not on to ironatoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, Imade

[gmx-users] single point calculation

  Hi, is my firt question in the list, i have a very simple and posibly a very nonsense question. do i have to use mdrun to performe a single point calculation of a certain conformation? how? is there something to specify in .mdp file? Can some body provide me an example of how to use ffscan

[gmx-users] Gromacs install question

Hi all, I have a question on installing gromacs: I have installed gromacs 3.3.1 on my computer. And it works. Today, I want to change one commands, so I reinstalled it in the following process: 1. remove the formal direcory of gromacs 2. change to the installation directory of gromacs 3. ./configu

[gmx-users] re: n-hexadecane simulation

1. Try the [ bonds ] section that I mentioned earlier and remove the [ constraints ] section. 2. Did you do an energy minimization? If so, what total Energy and max force do you acheive? 3. What is the size of your box? Is it >=3.0nm? Is that also larger than 1.49 + max_n-hexadecane_lengt

[gmx-users] a problem about Coul-LR in energy groups output. Coul-LR is always ZERO !

I want to analyze the energy during a normal simulation. Some strange things happened. In mdp file, I selected DNA, NA+, SOL for energy groups output. When I analyzed edr file by g_energy, I found Coul_LR is always ZERO. I think my parameters have no problem, rlist =  1.0 rcoulomb =  1.0, rv

Re: [gmx-users] re: n-hexadecane simulation

Thank you so much for your consideration. However, it still diverge even after correcting the number in 3rd column and using bond parameters. Also, using SHAKE is not helpful. I'm using single-precision GROMACS. Is it make this kind of problem? What else can I do try? Thank you in advance for yo

RE: [gmx-users] r.m.s.i.p

Try RMSD fit function. -Original Message- From: [EMAIL PROTECTED] on behalf of xi zhao Sent: Mon 9/18/2006 2:12 AM To: gmx-users@gromacs.org Subject: [gmx-users] r.m.s.i.p Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two

RE: [gmx-users] merger ligand and protein to constriant

Try the following way: But you shoul get you top file and gro file without the ligand. Then If your protein has 100 residues, add you ligand as residue 101 in the gro file. After residue add the "TER" . In ddition, adding the ligand ITP file to the later part of the Gro file. -Original

[gmx-users] protein unstable for parallel job while stable for serial one

Hello Has anybody seen a protein becoming unstable on parallel nodes while remaining stable on single node? I am running a NPT molecular dynamics simulation. The system contains a protein with 141 residues surrounded by water making the total to 32714 atoms. I ran this simulation at two places f

[gmx-users] Bonds

Hi!  I have a question . I am working with a proteina that they will count two centers FES co-ordinated for cisteins, these cisteins were not on to iron atoms, thus I modified the archive itp only with respect the bonds, no angles or diedrals, to bind to these two residuos. After the minimização, I

[gmx-users] re: n-hexadecane simulation

You have #2 in the 3rd column which nmeans that you are not excluding 1-2, 1-3, or 1-4 Nonbonded interactions as you are intended to. Change this value to a one instead of a two. That should fix your problem. However, I would recommend that you set up the regular RB bonds like this. That wa

Re: [gmx-users] n-hexadecane simulation

You could change the lincs_iter. I would use SHAKE rather than LINCS. For n-alkanes using the model of Ryckaert-Bellemans, it is OK. Anyway, 2fs is correct. Jae Hyun Park wrote: Dear all GROMACS users: I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic

[gmx-users] Re: Simulation problem with extended membrane system!

If you use the script as I have suggested, http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html The script is designed for a gro file that does not have any velocities written into it, ie. it looks like this: 1THR N1 0.801 6.473 -0.310 1THR H12 0.760

[gmx-users] n-hexadecane simulation

Dear all GROMACS users: I'm simulating n-hexadecane bulk at 300 K using UA model with fixed bond length, harmonic angle potential, and Rychaert-Bellemans torsion model. However, it is so unstable for 2fs time step - The bond length suddenly diverges. The simulation becomes stable for 0.2 fs tim

Re: [gmx-users] The molecule size

主月 ：） wrote: > Hi: > > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition . > > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too sm

Re: [gmx-users] short range nonbondeds = 0 in power4

Atte Sillanpää wrote: On Fri, 15 Sep 2006, Atte Sillanpää wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run u

Re: [gmx-users] short range nonbondeds = 0 in power4

On Fri, 15 Sep 2006, Atte Sillanpää wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No err

Re: 回复： Re: [gmx-users] r.m.s.i.p

HI Zhao, To compute RMSIP, you have to compute eigenvector using gromacs utility program then from that trajectory you can compute RMSIP using a script which I got from Tsjerk Wassenaar from this list. You can appraoch him. Regards, B.Nataraj On Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao" <

Re: 回复： Re: [gmx-users] r.m.s.i.p

Hi Xi Zhao, Please find attached a .csh script you can use to calculate the rmsip. The script is of the hand of Isabella Daidone, now in Heidelberg. Note that for a set of 'equal' simulations there is a spread in the values you obtain for the RMSIP (i.e. it's not an absolute measure of equality

回复： Re: [gmx-users] r.m.s.i.p

Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP).    Amadei, A., de groot, B. L., Ce

Re: [gmx-users] Re: Simulation problem with extended membrane system!

Thanks Chris, I really appreciate your help!I've got my extended membrane system regarding your note, and now I'm testing it with my GPCR. I am still not very familiar with the script, I think it will take some time to learn. Thanks again!On 9/13/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:>If

回复： Re: [gmx-users] r.m.s.i.p

Based on the essential dynamics analysis, the similar of the internal fluctuations in may simulation systems was evaluated by comparing principal subspace first 10 eigenvectors) of each structural trajectory by using the root mean square inner product(RMSIP).    Amadei, A., de groot, B. L., Ce

Re: [gmx-users] r.m.s.i.p

xi zhao wrote: > Dear Gromacs users: > I am a new gromacs user, I want ro calculate r.m.s.i.p > for exploring similar in motions of two different > proteins, I need a script or tools to calculate it. I > need your help! I don't know what r.m.s.i.p is. If you want to get help, please define careful

[gmx-users] r.m.s.i.p

Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! __