[gmx-users] Unit cell parameter and molecule volume calculation

Dear all I have a system with crystalline cellulose nanofibril in water. I simulate the system in constant pressure at different temperature. I want to know the unit cell parameter (a,b,c, alpha, beta, gamma) of the unit cell of tricilinic cellulose and also the density of cellulose at different te

[gmx-users] restart a stopped simulation after a power failure? correct command

Dear all, I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a stopped simulation after a power failure? I used the following command to restart the stopped simulation at 6.5 ns. *mdrun -s md.tpr -cpi state.cpt* Even Though the simulation appeared to be restarted successfully

[gmx-users] core dumped during equilibration in gromacs

Dear all, I am trying to simulate protein in urea box using "amber99sb-ildn" force field.During the equilibration following error occur-Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.27, max 0.000527 (between atoms 2089 and 2094) bonds that rotated more

[gmx-users] Help: Illegal divion by zero lipid+protein+solvent

Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid t

[gmx-users] Illegal divion by zero lipid+protein+solvent

Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid type

[gmx-users] simulation of molecules in solid state

Dear Users, I have a .cif (Crystallography Information File) of a crystal of charged molecules along with counter ions. I want to simulate it to study its stability at room temperature. Is this possible in GROMACS. If so, how is it done? Thanks & regards, Saumyak --

Re: [gmx-users] gmx sans and gmx saxs

Here is an interesting paper http://www.sciencedirect.com/science/article/pii/S0006349509002082 -- 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.gromacs.org/Support/Mailing_Lis

Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Just to list the ways that such a thing could happen: 1. change to $GMXLIB 2. change to the version of gromacs you are using or just a change to a different installation (so you have a different top directory) 3. you automate grompp by piping in a number and some change to #1 or #2 above has aff

[gmx-users] gmx sans and gmx saxs

Dear gromacs users, I am trying to calculate static structure factor from the MD trajectory. I want to calculate this from the trajectory and not simply by Fourier transform of g(r). Can someone please tell me how to do this using gromacs ? Can I use gmx sans ? What is gmx saxs ? (are there neutr

[gmx-users] Reply To: Fatal Error - XTC error - maybe you are out of disk space?

Thank you so much for your response, Justin. Please is there something I can do to fix this? Or is it beyond my control? > > -- Best wishes, Kelechi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Ca

Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Well, yes. I have been preparing .tpr files in the exact same way for the last 6 months or so when I was getting the correct occupancies with these corrections. There were no errors whatsoever.  In fact, when I delete the non-bonded salt bridge corrections from ffnonbonded.itp, I get considerabl

Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

On 4/17/17 6:09 AM, Priyesh Mohanty wrote: I've also tried increasing the sigma to higher values beyond 0.325 which should in principle considerably weaken salt bridges but there appears to be no decrease in salt bridge occupancy despite the increase in sigma. It is as though mdrun is not re

Re: [gmx-users] Error in pdb2gmx command (Justin Lemukel)

On 4/17/17 3:24 AM, Yogendra Patel wrote: Hello gromacs users, I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs 4.5.5. While running the pdb2gmx to generate the topology, I'm getting the error as follows. I have kept the modified rtp file, pdb file and modified ffbonde

Re: [gmx-users] Fatal Error - XTC error - maybe you are out of disk space?

On 4/16/17 9:16 PM, Kelechi Okoroafor wrote: Thank you so much, Christopher. The simulations were running on my personal computer, specifically /media/OkwuchisHDD The command "df" returns: *** Filesystem 1K-blocks Used Available Use% Mounted on udev

Re: [gmx-users] Use of LINCS during production run

On 4/14/17 1:55 PM, Saumyak Mukherjee wrote: Dear users, Can you please inform me, which LINCS condition (h-bond, all bonds etc.) should be used during final production run to get the most realistic results? The constraints should be assigned based on what the force field prescribes, becau

Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

I've also tried increasing the sigma to higher values beyond 0.325 which should in principle considerably weaken salt bridges but there appears to be no decrease in salt bridge occupancy despite the increase in sigma. It is as though mdrun is not reading the nonbonded_param addition correctly.

[gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

Dear all,I've been using certain non-bonded corrections to the strength of salt bridges in this forcefield based on a recent publication for the last 6 months or so. The following correction was added to the ffnonbonded.itp file which increases sigma from 0.310 to 0.318 : [ nonbond_params ]N3 

Re: [gmx-users] Error in pdb2gmx command (Justin Lemukel)

Hello gromacs users, I made a force field (rtp) file for my polymer using CHARRM 27 in gromacs 4.5.5. While running the pdb2gmx to generate the topology, I'm getting the error as follows. I have kept the modified rtp file, pdb file and modified ffbonded.itp file in my working folder. The rtp file