[gmx-users] Re: Extend water layer along negative Z-direction

Hi ALL, Thanks a lot Chris, Justin and Tsjerk for yor replies. Actually, my problem is not fully resolved. A portion of the protein tail is outside the water box in the Z direction (coordinate in Z is -35). So as suggested by you when I am issuing the command editconf -f box.gro -o BOX.gro

Re: [gmx-users] Re: Extend water layer along negative Z-direction

Hi Anirban, You have to get a grip on PBC. What you're suggesting is like extending the earth only westward, but not eastward as something is sticking out in only one direction. It's impossible! The system is periodic.The box vectors are direction vectors, indicating the periodicity. Moreover,

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. My command lines are: $grxdir/grompp -f 4AKEpreEMcg.mdp

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

On Jun 1, 2009, at 1:12 PM, Stefano Meliga wrote: Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. My

[gmx-users] crystals of KCl during simulation

Hi, I am trying to simulate a protein in aqueous solution 1M (KCl) with Gromacs and using the amber force field. I get the topology of the solvated protein - without the ions- from amber (Leap) and then used the script amb2gmx.pl to obtain the Gromacs .top and .gro files. I did not introduced

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Stefano Meliga wrote: Hi again, The energy minimization with conjugate gradient integrator still gives me two warnings of the type: t = 0.011 ps: Water molecule starting at atom 28122 can not be settled. Check for bad contacts and/or reduce the timestep. OK I checked the code, and

Re: [gmx-users] crystals of KCl during simulation

Rebeca García Fandiño wrote: Hi, I am trying to simulate a protein in aqueous solution 1M (KCl) with Gromacs and using the amber force field. I get the topology of the solvated protein - without the ions- from amber (Leap) and then used the script amb2gmx.pl to obtain the Gromacs .top and

Re: [gmx-users] crystals of KCl during simulation

Hi, rega...@hotmail.com said: [..] but after equilibration I have observed that KCl is aggregating, like if it was making crystals. When I used NaCl instead KCl, this not happened. Does anybody has any idea about the reason of the behaviour of KCl in the simulation? This even does happen

[gmx-users] Extend water layer along negative Z-direction

Hi Anirban, I suspect that your problem is that you define a box with zero x, zero y, and a negative z. I think it's time to read the manual. Hi ALL, Thanks a lot Chris, Justin and Tsjerk for yor replies. Actually, my problem is not fully resolved. A portion of the protein tail is outside the

RE: [gmx-users] crystals of KCl during simulation

Thank you very much for your answer. I have read some recent literature, and you are right, it is a problem about the parameters for ions in Amber. I have found this paper: Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of Inaccuracies and Proposed Improvements

Re: [gmx-users] crystals of KCl during simulation

Rebeca García Fandiño wrote: Thank you very much for your answer. I have read some recent literature, and you are right, it is a problem about the parameters for ions in Amber. I have found this paper: Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of Inaccuracies and

RE: [gmx-users] crystals of KCl during simulation

Yes, I use PME. Date: Mon, 1 Jun 2009 19:34:27 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] crystals of KCl during simulation Rebeca García Fandiño wrote: Thank you very much for your answer. I have read some recent literature, and you are

RE: [gmx-users] crystals of KCl during simulation

Hi Rebeca, I found out a few years ago that OPLS parameters for Na+ were inadequate for my simulations on surfactants aggregation due to the formation of stable (and unrealistic) ionic bridges. I got better structures using Aqvist's parameters (available in GROMACS), maybe you could try these

Re: [gmx-users] crystals of KCl during simulation

Rebeca García Fandiño wrote: Thank you very much, André. Could you please indicate me how could I use these parameters in Gromacs? I have not seen them included in ions.itp and I could not find anything in the manual. Best wishes, Rebeca. I would recommend reading the following paper,

[gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

Hi,gmx-users I am running a editconf commond like this, editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro but I am getting the following the fatal error: Fatal error: Library file aminoacids.dat not found in current dir nor in default directories. (You can set the directories to search with the

Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

Jinyao Wang wrote: Hi,gmx-users I am running a editconf commond like this, editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro but I am getting the following the fatal error: Fatal error: Library file aminoacids.dat not found in current dir nor in default directories. (You can set the

[gmx-users] Re: gmx-users Digest, Vol 62, Issue 4

Hi Rebeca: If you wish to replicate the settings of http://pubs.acs.org/doi/abs/10.1021/jp0765392 (Aqvist's ions in AMBER) then you need the following LJ cross-types specified in your non-bonded forcefield or topology file, which were generated using geometric mixing rule instead of the