[gmx-users] pdb2gmx: Adding non standard residues and molecular moieties

Greetings I am trying to generate a topology file, and need to add the phosphate ion in my pdb How to do this? Thanks eduardo Graduate minion some random prestigious program ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] Gro file with more than 99999 atoms

Dear ALL; I'm converting a file into a gro format but it has more than 9 atoms. How should I handle the first and fourth columns since I should keep them to five digits only? Thanks, Adama ___ gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] Change in .gro in grompp

Caleb Carlin wrote: Greetings, I am simulating tip4p-ICE between two slabs of silicon. Prior to using grompp, the configuration renders correctly in VMD and appears as intended. After using grompp and mdrun, the system errors out with LINCS errors. The recorded configuration steps show the si

Re: [gmx-users] Change in .gro in grompp

Quoting Caleb Carlin <[EMAIL PROTECTED]>: > Greetings, > I am simulating tip4p-ICE between two slabs of silicon. Prior to using > grompp, the configuration renders correctly in VMD and appears as intended. > After using grompp and mdrun, the system errors out with LINCS errors. The > recorded co

[gmx-users] Change in .gro in grompp

Greetings, I am simulating tip4p-ICE between two slabs of silicon. Prior to using grompp, the configuration renders correctly in VMD and appears as intended. After using grompp and mdrun, the system errors out with LINCS errors. The recorded configuration steps show the silicon slabs pushed toget

[gmx-users] RE: RE : FEP : separating components of dgdl

> Date: Tue, 5 Feb 2008 18:25:17 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: RE : FEP : separating components of dgdl > > > Thanks Berk, everything is fine at last. > I guess this is my last question : if for example I change three bond lengths > from b0A=0.1 to b

[gmx-users] Total energy of protein only

Hi gmx-users, Can anyone tell me how to find the total energy of the protein only (not the system)? You might try energygrp_excl SOL SOL or energygrp_excl SOL SOL SOL PROTEIN depending on what you want to acheive. THis will take care of all of the nonbonded interactions. Without knowing wha

[gmx-users] Re: WARNING concerning lipid.itp

And again I will support myself :-) If you want to get more replies, you should include some more detailed information and also search the archives first (e.g. you might have found this: http://www.gromacs.org/pipermail/gmx-users/2002-July/001986.html by searching Overriding LJ-14 para

[gmx-users] RE : FEP : separating components of dgdl

Thanks Berk, everything is fine at last. I guess this is my last question : if for example I change three bond lengths from b0A=0.1 to b0B=0.15, when I use gmxcheck with -ab, it prints only one difference between state A and B, instead of 3. Is this ok ? Maik, what is the power you are using

[gmx-users] Total energy of protein only

Hi gmx-users, Can anyone tell me how to find the total energy of the protein only (not the system)? What I've done is I minimized the system first, then I took out the water from the pdb file, then minimized it again without water, and get the total energy from the log file. But when I'm comparin

[gmx-users] Re: WARNING concerning lipid.itp

And again I will support myself :-) So, as I learnt so far, for this effect the topology file is responsible. In the included force fields the described LJ 1-4 parameters does not correspond to the LJ parameters of the OW OW interaction of the lipid.itp which gets included after these force fie

[gmx-users] Re: Warning: pressure scaling more than 1%

Dear gmx-users. It is a pity no one wanted to help me, but I have found the answer by myself and want to share it with you... For the problem with the pressure scaling more than 1% I can recommend to use the following link: http://wiki.gromacs.org/index.php/error After increasing the tau_p up

[gmx-users] Re: Warning: pressure scaling more than 1%

Dear gmx-users. It is a pity no one wanted to help me, but I have found the answer by myself. For the problem with the pressure scaling more than 1% I can recommend to use the following link: http://wiki.gromacs.org/index.php/error After increasing the tau_p up to 1.0 ps the Simulation worked

Re: [gmx-users] segmentation fault (wrong settings in mdp file)

> Quoting Louic Vermeer <[EMAIL PROTECTED]>: > >> On Tuesday 5 February 2008 14:02, Egidijus Kuprusevicius wrote: >> > I know that something is wrong with my mdp file, >> > but do not know what exactly can cause it (what parameters I should do >> not >> > use or use instead). >> It would help to in

Re: [gmx-users] segmentation fault (wrong settings in mdp file)

Quoting Louic Vermeer <[EMAIL PROTECTED]>: > On Tuesday 5 February 2008 14:02, Egidijus Kuprusevicius wrote: > > I know that something is wrong with my mdp file, > > but do not know what exactly can cause it (what parameters I should do not > > use or use instead). > It would help to include your

Re: [gmx-users] segmentation fault (wrong settings in mdp file)

On Tuesday 5 February 2008 14:02, Egidijus Kuprusevicius wrote: > I know that something is wrong with my mdp file, > but do not know what exactly can cause it (what parameters I should do not > use or use instead). It would help to include your mdp file in your message.

[gmx-users] segmentation fault (wrong settings in mdp file)

Dear All, maybe anyone knows why I'm getting a 'segmentation fault' error while I'm running mdrun. I know that something is wrong with my mdp file, but do not know what exactly can cause it (what parameters I should do not use or use instead). Thank you in advance

Re: [gmx-users] Source code file: gmxfio.c, line: 784

Am Dienstag, 5. Februar 2008 schrieb Mark Abraham: > > Fatal error: > > Can not read/write topologies to file type trr > > --- > > > > i got one hit regarding my query from archive which iam not able to > > resolve.hear iam attaching the link

[gmx-users] RE:Source code file: gmxfio.c, line: 784

hiii thank for your reply mark sory for pasting other url iam using gromacs 3.3 version on sunsolaris platform,my protein contain 86 aminoacid and iam trying to unfold it at 640k hear iam pasting the command which i was used for final mdrun grompp -c 1HB6M_pr.gro -p 1HB6M.top -o 1HB6uf_b4full.tpr

Re: [gmx-users] Source code file: gmxfio.c, line: 784

> Hi all, > > iam trying to unfold 86 amino acid contain peptide at 640k . > but my final mdrun terminated with following error: > - > 15 steps,300.0 ps. > > step 22790, will finish at Tue Feb 5 19:41:24 2008- > Program mdrun, VE

RE: [gmx-users] How to obtain the temperature from a given trajectory

> Date: Tue, 5 Feb 2008 07:41:44 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] How to obtain the temperature from a given trajectory > > Dear all, > I have some old trajectories trr files containing coordinates and velocities

[gmx-users] RE: FEP : separating components of dgdl

> Date: Mon, 4 Feb 2008 16:18:53 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: FEP : separating components of dgdl > > > > Thanks Maik for your parameters for amber99 soft core ! > > Berk, you were right. The missing term is

[gmx-users] Source code file: gmxfio.c, line: 784

Hi all, iam trying to unfold 86 amino acid contain peptide at 640k . but my final mdrun terminated with following error: - 15 steps,300.0 ps. step 22790, will finish at Tue Feb 5 19:41:24 2008- Program mdrun, VERSION 3.3 Source

Re: [gmx-users] FEP : separating components of dgdl

Hi This warning is really strange. You could try to execute grompp with -pp to get the preprocessed topology and have a look, if the the B-parameters are included correctly. As far as I know, it should; I do it the same way. Anyway, you could also explicitly take the parameters for that dihedra