[gmx-users] Re: Energy minimizations taking really, really long?

It depending the time steps that u used or the molecule that u had is big..Thats why ur EM take a long time..Is better take a long time rather than quick but had a lot of errors.. On Wed, Oct 23, 2013 at 9:59 AM, Nimmy McNimmerson [via GROMACS] ml-node+s5086n5011918...@n6.nabble.com wrote: I

[gmx-users] Re: multiple chain

Thanks Justin for the quick reply. by the way after i solvated the protein with water and i change the amount of the protein that i want for example 8 and the amount of water that already in is 20453.But after i proceed with grompp the result shows that my .top file have different number of

[gmx-users] Re: segemntation fault after run do_dssp

Hi Eric, I'm using gromacs 4.5.5. Is it the version is different for dssp? Thanks On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS] ml-node+s5086n5008885...@n6.nabble.com wrote: HI, What version of gromacs is this? DSSP changed its syntax a while back and we had to adjust do_dssp

[gmx-users] Re: NVT and NPT for small peptide

Hi Maggin, It depend on your protein stability..It can be short or long..Check the .edr file by using g_energy On Thu, May 23, 2013 at 9:44 AM, maggin [via GROMACS] ml-node+s5086n5008461...@n6.nabble.com wrote: Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need for NVT

[gmx-users] Re: combine two gro files

Thanks Dr. Dallas for your replying. But my friend told me that the extended one is only 2 ns not the total 22ns. So,the gro for the extended one is not affect at all? I thought that the gro file that prodice from the extend one is only 2 ns. Thanks Doc! On Wed, Mar 13, 2013 at 11:19 AM,

[gmx-users] Re: grompp error

minimize -v Need to edit the em1.mdp by using the highest emtol starting from 1000 and decrease it little by little to get the lowest energy. Regards, SHika On Tue, Oct 23, 2012 at 11:14 AM, Nur Syafiqah Abdul Ghani pqah...@gmail.com wrote: Okay thanks for the explanation Justin. But,i would

[gmx-users] Re: Fwd: How to can i replace a molecule

twice On Mon, Oct 8, 2012 at 9:21 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5001768...@n6.nabble.com wrote: On 10/7/12 9:17 PM, shika wrote: Thanks Justin. May I ask something, if i'm using the command for genbox before minimization which is genbox -cp protein_box.gro -cs solvent.gro -p