[gmx-users] error in running systems in parallel

Hai Friends, I have individual input files and directories for my system, i want to perform REMD(replica exchange MD). when i execute multiple simulation run mdrun_mpi, gets a error like this: I have individual directories called equil0, equil1, equil2, equil3 which contains input/output fi

Re: [gmx-users] Amber to Gromacs

On 4/30/14, 12:17 PM, Nash, Anthony wrote: Hi Justin, I wonder if you could advice, I am a little further ahead than I was before. I am using an crystal structure .pdb from the protein data bank. There are no hydrogen atoms. I assume, given the pdb2gmx that this is taken care of unless the

Re: [gmx-users] Amber to Gromacs

Hi Justin, I wonder if you could advice, I am a little further ahead than I was before. I am using an crystal structure .pdb from the protein data bank. There are no hydrogen atoms. I assume, given the pdb2gmx that this is taken care of unless the -ignh is selected. I am getting a painful erro

Re: [gmx-users] Azurin protein attached to metal atom of Cu.

On 4/30/14, 9:59 AM, Nicola Staffolani wrote: How are you treating the bonds during the simulation? If you're using "constraints = all-bonds," then this is precisely the outcome you should expect; all the requested bonds are indeed present and are being kept fully rigid by the constraint algor

Re: [gmx-users] Azurin protein attached to metal atom of Cu.

> How are you treating the bonds during the simulation? If you're using > "constraints = all-bonds," then this is precisely the outcome you should > expect; all the requested bonds are indeed present and are being kept fully > rigid by the constraint algorithm. If there were no bond(s) produced b

Re: [gmx-users] Amber to Gromacs

Wow! I am out of date. As always, thanks for the help Justin. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2014 13:29 To: gmx-us...

Re: [gmx-users] Questions about g_energy output values Coul-SR, LJ-SR, Coul-14, LJ-14

On 4/30/14, 8:56 AM, Vytautas Rakeviius wrote: First I want to ask for explanation what SR and 14 means? It is explained briefly in docs, but I want longer explanation if possible. SR = short-range, within the nonbonded cutoff (rcoulomb or rvdw). 14 = 1-4 interactions, i.e. intramolecular

[gmx-users] Questions about g_energy output values Coul-SR, LJ-SR, Coul-14, LJ-14

First I want to ask for explanation what SR and 14 means? It is explained briefly in docs, but I want longer explanation if possible. Also I want to ask to be sure positive value of those outputs means attraction and negative repulsion right? -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Amber to Gromacs

On 4/30/14, 8:25 AM, Nash, Anthony wrote: Hi All, I've been thrown upon a project which requires the use of the Amber FF. I have a crystal structure .pdb and I wish to make a topology file using the AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports program, which

[gmx-users] Amber to Gromacs

Hi All, I've been thrown upon a project which requires the use of the Amber FF. I have a crystal structure .pdb and I wish to make a topology file using the AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports program, which seems to require Gromacs versions 3.1.4, 3.2.1

Re: [gmx-users] special bond

On 4/30/14, 4:53 AM, Nicola Staffolani wrote: ​​Hi Justin, thank you very much for caring! ​ On Tue, Apr 29, 2014 at 6:19 PM, Justin Lemkul wrote: It would be helpful to see: 1. The actual error messages. 2. The lines of the topology to which they correspond. ​ ​ *ERROR 1 [file spep

Re: [gmx-users] Azurin protein attached to metal atom of Cu.

Please keep the discussion on the gmx-users mailing list. On 4/30/14, 6:37 AM, Alessia Giuliani wrote: hello, first of all thanks for reply. I send to you the specialbond.dat : 11 CYSSG1 CYS SG1 0.2CYS2CYS2 CYSSG1HEM FE2 0.25CY

Re: [gmx-users] Write a pdb file after every ns of simulation

Hi Tsjerk, Hi, just noticed, I used the wrong group. Up and running now. Thanks On Wed, Apr 30, 2014 at 11:56 AM, Tsjerk Wassenaar wrote: > > What am I missing? > > > > > The ligand! (Oh, I just couldn't resist! Sorry about that.) > > Either your xtc-groups weren't set correctly or your index gr

Re: [gmx-users] Write a pdb file after every ns of simulation

> What am I missing? > > The ligand! (Oh, I just couldn't resist! Sorry about that.) Either your xtc-groups weren't set correctly or your index group does not include the ligand. I hope for you it's the latter. Cheers, Tsjerk -- Gromacs Users mailing list * Please search the archive at http:/

Re: [gmx-users] Write a pdb file after every ns of simulation

Hi, What were your xtc groups in the map file? Perhaps you didn't include the ligand. Yours, Erik On 30 Apr 2014, at 10:42, MUSYOKA THOMMAS wrote: > Thanks Tsjerk, > I have a 10 ns protein-ligand MD simulation and want to extract a pdb > structure (protein-ligand) at every nanosecond time po

Re: [gmx-users] Write a pdb file after every ns of simulation

Thanks Tsjerk, I have a 10 ns protein-ligand MD simulation and want to extract a pdb structure (protein-ligand) at every nanosecond time point, So I used the following command trjconv -f md_fit.xtc -s ../md.tpr -sep -dt 1000 -o out.pdb and selected the protein | ligand group However, when I open

Re: [gmx-users] Write a pdb file after every ns of simulation

Hi Musyoka, Provided you saved enough: trjconv -dt 1000 Cheers, Tsjerk On Wed, Apr 30, 2014 at 9:46 AM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Dear Users, > I want to write a pdb file after each ns of my 10 ns protein-ligand > trajectory > Which command do I use? > Thank yo

Re: [gmx-users] special bond

​​Hi Justin, thank you very much for caring! ​ On Tue, Apr 29, 2014 at 6:19 PM, Justin Lemkul wrote: > > It would be helpful to see: > 1. The actual error messages. > 2. The lines of the topology to which they correspond. > ​ > ​ *ERROR 1 [file speptide.top, line 3224]: No default G96Bond typ

Re: [gmx-users] pdb2gmx, charmm22 and HEME

On 29 Apr 2014, at 23:32, Justin Lemkul wrote: > > > On 4/29/14, 5:13 PM, Erik Marklund wrote: >> Dear users, >> >> I am trying to preprocess a cytochrome C structure with pdb2gmx and have run >> into some problems. The forcefield has parameters for the HEME group, but >> other components

[gmx-users] Write a pdb file after every ns of simulation

Dear Users, I want to write a pdb file after each ns of my 10 ns protein-ligand trajectory Which command do I use? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gro

Re: [gmx-users] gromacs 5.0

Hi, the g_membed tool is integrated in mdrun now. Try gmx mdrun -membed membed.dat Best, Carsten On 30 Apr 2014, at 03:41, gejingming <531015...@qq.com> wrote: > dear sir, > now ,I am using gromacs 5.0 VERSION ,but there is not g_membed and tpbconv > commond.I think it is important for us.