Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Just to add to the above post, running a none to vdw-q tranformation using the following parameters also results in the same error for simulation at first lambda.

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Hello GROMACS users, As Wes had advised previously in this thread, the issue with the vdw tranformations was rectified by removing the charges from the topology file. Thereafter, I also tried running free energy calculations using the following free-energy parameters:

[gmx-users] Fwd: Can a mutation make a protein stable - result analysis from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

[gmx-users] Free Energy Calculations with Position Restraints

Hello all, Is there a way to use the free energy code with position restraints (similar to the way that the free energy code interacts with the pull code)? From the manual all I can see that might be relevant is "restraint-lambdas" but that is apparently only for "dihedral restraints, and the

[gmx-users] Can a mutation make a protein stable - result analysis from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 161, Issue 42

Hi, Justin thanks again for your reply! 1. The 352 water molecules in a .gro file was actually gotten. I have checked it by viewing the .gro file and by the VMD and Avogrado software. 2. Could the failure be caused by the out-of-box hydrogen atoms? (Some of H atoms are out of the definition box

Re: [gmx-users] dielectric constant -reg

Hi, Clearly the .mdp file changes you say you are making aren't showing up later in wherever you are observing a 1.12, but we'll need to see a lot more detail of your process - e.g. command lines with the file names - to suggest what might be wrong. That means you need to be able to copy and

[gmx-users] Can a SNP mutation make a protein stable - result from GROMACs run

Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said that the mutant has made the complex more

Re: [gmx-users] DSSP executable

Thanks Marc! On Mon, Sep 11, 2017 at 6:07 PM, Mark Abraham wrote: > Hi, > > You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first > two > sentences are useful for you ;-) > > Mark > > On Mon, Sep 11, 2017 at 5:05 PM Deep kumar

Re: [gmx-users] DSSP executable

Hi, You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first two sentences are useful for you ;-) Mark On Mon, Sep 11, 2017 at 5:05 PM Deep kumar wrote: > Hello All, > > Can someone please help me get the "dssp" executable? For secondary > structure

[gmx-users] DSSP executable

Hello All, Can someone please help me get the "dssp" executable? For secondary structure analysis. I did this: rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/ This downloaded all dssp pdb files but no executable. I am doing this because I got the error on gromacs run. Fatal error:

Re: [gmx-users] gromacs error

Hi, Yeah I've never seen that, so I assume it's something weird related to how GROMACS was originally compiled vs how the system has been updated since. Since a rebuild is the way to investigate that, definitely update to at least the latest 5.0.x while you do it. Mark On Mon, Sep 11, 2017 at

Re: [gmx-users] Protein break after simulation

no grompp not gives any warning neither i have used -maxwarn option. On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul wrote: > > > On 9/11/17 2:43 AM, ISHRAT JAHAN wrote: > >> how can i check whether the structure is whole or not in .tpr file? After >> trjconv whole stage i got

Re: [gmx-users] gromacs error

On Mon, Sep 11, 2017 at 8:44 AM, Vidya R wrote: > Hi, > > > When I give these two commands > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > gmx mdrun -deffnm min > > I get this error. > > What to do? > > > > Reading file min.tpr, VERSION 5.0.2 (single precision) >

[gmx-users] gromacs error

Hi, When I give these two commands gmx grompp -f mdp/min.mdp -o min -pp min -po min gmx mdrun -deffnm min I get this error. What to do? Reading file min.tpr, VERSION 5.0.2 (single precision) tMPI error: tMPI Initialization error (in valid comm) Thanks, Vidya.R -- Gromacs Users mailing

Re: [gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.

On 9/11/17 1:53 AM, Yanke Peng wrote: Hi, Justin, Thanks very much for your advice. I think I should try a low concentration NaCl to verify if the system has the chance to be energy minimizated. Here are the exact commands that I used. 1. solution definition #water box and topology file

Re: [gmx-users] Module for spectroscopy analysis

On 9/11/17 2:28 AM, Joel Awuah wrote: Hi gromacs user, I want to perform a spectroscopic analysis of amino acids. Is there any module in gromacs to help me with that. Sounds more like a quantum mechanical question, so no, not really. -Justin --

Re: [gmx-users] Protein break after simulation

On 9/11/17 2:43 AM, ISHRAT JAHAN wrote: how can i check whether the structure is whole or not in .tpr file? After trjconv whole stage i got broken structure. This is beyond just a "broken" structure.  No amount of PBC manipulation will fix this; it's as if the topology wasn't sound and you

Re: [gmx-users] HPC performance in Gromacs ?

Hi, More threads can help, but unless I miscounted, the number of threads you started in your previous run was larger than the number of cores (i.e. you oversubscribed the CPU cores). That will never be beneficial with GROMACS. The run stats look more reasonable now, but your run still starts

Re: [gmx-users] GPU-accelerated EM

I'm still not sure why would the GPU-accelerated EM runs slower than the CPU-only run -- unless the GPU in question is at best as fast at computing nonbonded interactions as the CPU (cores) assigned to the job. Have you looked at log files? -- Szilárd On Sat, Sep 9, 2017 at 1:33 AM, Alex

Re: [gmx-users] dielectric constant -reg

Hi, Change the mdp file and use that file to make a new tpr file and that the file to run a simulation. Mark On Mon, 11 Sep 2017 08:21 Meagha ramana kumar wrote: > Hi gmx-users, > > My problem may sound silly, but please help me with it. I know how to > change dielectric

Re: [gmx-users] Fatal error : Domain Decomposition

Hi, There is a URL in the error message that gives us you some suggestions, but the primary one is in the message: use fewer nodes. A small simulation cannot be usefully parallelised over large amounts of hardware. Mark On Mon, 11 Sep 2017 08:47 Juriti Rajbangshi wrote:

Re: [gmx-users] Protein break after simulation

Here i am providing you the link of protein structure https://we.tl/X4yEyZq2aR On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul wrote: > > > On 9/10/17 3:27 AM, ISHRAT JAHAN wrote: > >> Dear Justin >> I have used all the commands given in the link provided by you but unable >> to

[gmx-users] Fatal error : Domain Decomposition

Hi, I have found an error when running simulation of an ionic liquid using 256 nodes. So, how can I change the mdrun options to run the simulation in higher nodes? Fatal error: There is no domain decomposition for 192 nodes that is compatible with the given box and a minimum

Re: [gmx-users] Protein break after simulation

how can i check whether the structure is whole or not in .tpr file? After trjconv whole stage i got broken structure. On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham wrote: > Hi, > > You seem to reporting that your system isn't whole. Is it whole after the > trjconv

[gmx-users] Module for spectroscopy analysis

Hi gromacs user, I want to perform a spectroscopic analysis of amino acids. Is there any module in gromacs to help me with that. Kind regards Joel -- Joel Baffour Awuah PhD Candidate *Institute for Frontier Materials* *Deakin University* *Waurn Ponds, 3126 VIC* *Australia +61450070635

[gmx-users] dielectric constant -reg

Hi gmx-users, My problem may sound silly, but please help me with it. I know how to change dielectric constant for simulation. Yes I have read all the previous thread reading this and no one provided straight answer to this. I am using PME. I tried changing all the epsilon values but nothing