[gmx-users] Charge Correction using HF method

Dear Justin Sir I am doing protein and drug MD simulation. I have generated the itp file of drug from PRODRG. I have calculated the charge on the atom using HF/6- 31G* basis set from orca3.0. Is this a right protocol to use it in GROMACS for the charge correction. With Regards Tasneem -- Gromacs

[gmx-users] Charged systems

Dear all, I have a system containing one positively charged ion frozen at the centre of the box with water molecules and one negatively charged ion in bulk water. However, the overall change in my system is not neural. I am using PME electrostatics and running the simulation. I wanted to know

[gmx-users] How to solve OXT atom (termial oxygen atom) issue?

First of all I am extremely sorry for my mistake. I haven't sent you the modified coordinate file. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen ch

[gmx-users] Protein-Ligand Complex MD simulation

We have a 419 amino acid long protein and planned for Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What fact

[gmx-users] Protein-Ligand Complex MD simulation

Dear all, We have a 419 amino acid long proteing and planned Protein-ligand complex MD simulation using Gromacs 5.1.4 to check. —Whether the protein and inhibitor complex stable —Did the inhibitor remain in the active site pocket or did it fall out during the simulation —What factors contributed t

Re: [gmx-users] Energy group exclusions

Thanks a lot for the reply. Regards Sukriti [https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%

Re: [gmx-users] constraint

Thank you sir for your reply. Methanol is my next phase of my project. I forget to remove the final line. On Fri, Dec 16, 2016 at 2:23 AM, Mark Abraham wrote: > Hi, > > Like the warning says, you need a smaller time step or bond constraints. > I'm sure that whoever designed this model had one

Re: [gmx-users] Inconsistent shifts

Dear Justin, Thank you very much. Best regards, Mijiddorj > > On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much for reply. > > My commands > > > > gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump > > gmx trjconv -s ../step7_1.tpr

Re: [gmx-users] CG Lincs errors

Alex and Mark, thanks for the information. I’ll drop dt down, significantly, drop the temperature, and run it for a long time. Thanks for the ideas. Anthony On 15/12/2016 21:54, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alex" wrote: >Mark is right, no two ways about it.

Re: [gmx-users] CG Lincs errors

Mark is right, no two ways about it. For initial equilibration and assessing preexisting structural strains try vacuum, _much_ smaller timesteps and possibly low temperatures in vacuum, only then transfer to solvent, etc. Algorithmically, LINCS requires convergence and you already are using a prett

Re: [gmx-users] GROMACS 5.1.2 performance

Hi, Something about your job start-up is a) strange and b) not what you asked for. Get one node working in a way that you understand. Then two. Mark On Wed, 14 Dec 2016 23:57 Justin Lemkul wrote: > > > On 12/14/16 6:44 AM, Neha Gandhi wrote: > > Dear list, > > > > I think the question on groma

Re: [gmx-users] Energy group exclusions

Hi, As you've seen in http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html#energy-group-exclusions such exclusions are only for efficiency, which would make negligible impact here. And anyway the bonds in your molecule probably generate nonbonded exclusions within that molecule

Re: [gmx-users] CG Lincs errors

Hi, If a simulation isn't stable with a small time step (as I think you are saying) then moving to a larger time step is guaranteed to make that worse. Try an even smaller time step, for a long time, and see what happens. Or take a subset of your protein and see what happens. Or simulate in vacuo

Re: [gmx-users] To trjcat or not to trjcat

Hi Mark, I have implemented what Justin suggested -- works perfectly fine (thanks Justin!). I am very bad at bash scripting, but this was simple even for me. However, what you are suggesting may become extremely useful later on, both in terms of using trjcat and dealing with repeated back-to-back

Re: [gmx-users] constraint

Hi, Like the warning says, you need a smaller time step or bond constraints. I'm sure that whoever designed this model had one of those in mind and you are closely consulting what they wrote :-) Mark On Thu, 15 Dec 2016 23:20 NIKHIL JOSHI wrote: > GMX Users: > > When I run grompp on Polyetylen

Re: [gmx-users] To trjcat or not to trjcat

Hi, You wanted automatic, which Justin's sequence achieves via writing a script. But you can render trjcat non-interactive and that might be easier. See http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Probably you can make your life even easier in future by judicious use of

Re: [gmx-users] Free Energy Landscape- PCA

Hi, The trjconv -drop* functionality is useful here. IIRC it only does a 1D form, but you can do two stages of that. Mark On Fri, 16 Dec 2016 02:36 Romero, Raquel wrote: > Thanks a lot, I know how to do it now, so each value given in the > 2dproj.xvg corresponds to a time step of the simulatio

[gmx-users] trajectory analysis

Dear gromacs users.. I have the following questions. 1) ::how i analyse trajectory using VMD? 2)::Trajectory analysis for overall protein structure stability?? 3)::protein - ligand interaction i-e H-bonds and anyother interactions.?? 4)::trajectory analysis for free energy binding of protein and

Re: [gmx-users] Free Energy Landscape- PCA

Thanks a lot, I know how to do it now, so each value given in the 2dproj.xvg corresponds to a time step of the simulation, right? so if I delimit the area in the FEL of which I want to know the coordinates i can extract all the frames that correspond to those eigenvalues by searching in the fil

Re: [gmx-users] Desolvation or hydration free energy of an ION

Thanks Justin for your response. Surly PMF is better, but the point is that via FEP I have already calculate the binding free energy of a charged amino acid to a solid surface while Na+ used as counter-ion where both "amino acid and Na+" considered as a single "couple-moltype" to be decoupled both

Re: [gmx-users] To trjcat or not to trjcat

Since the first frame of trajectory (N+1) will be the same as the last frame of trajectory N, then you need to do two things: 1. Use trjconv -b 50 to remove the first frame from all but the first trajectory. This eliminates the duplicate frames. 2. Then use trjconv -t0 to set a new start tim

Re: [gmx-users] Free Energy Landscape- PCA

On 12/15/16 10:02 AM, Romero, Raquel wrote: Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem You (presumably) constructed a time series of eigenvalu

Re: [gmx-users] Free Energy Landscape- PCA

Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem > On 14 Dec 2016, at 12:49, Justin Lemkul wrote: > > > > On 12/12/16 9:30 AM, Romero, Raquel wrot

Re: [gmx-users] Desolvation or hydration free energy of an ION

On 12/15/16 9:39 AM, Alex wrote: Hello gromacs user, I was wondering if anybody has experience with the hydration or desolvation free energy of an ION for example Na+, using alchemical free energy perturbation method? Actually in my case, I would like to calculate the difference between free

Re: [gmx-users] To trjcat or not to trjcat

On 12/14/16 7:23 PM, Alex wrote: Hi all, I have 20 simulated trajectories of equal duration (10 ns, frames are output every 50 ps), each subsequent simulation started from the output .gro of the previous. I can explain why, but it's likely to be immaterial. The goal is to have one complete tr

Re: [gmx-users] Inconsistent shifts

On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote: Dear Justin, Thank you very much for reply. My commands gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol -ur compact -n ../index.ndx -fit transxy -o md_noPBC.xtc I g

[gmx-users] Desolvation or hydration free energy of an ION

Hello gromacs user, I was wondering if anybody has experience with the hydration or desolvation free energy of an ION for example Na+, using alchemical free energy perturbation method? Actually in my case, I would like to calculate the difference between free energy of "Na+" when it is close to a

Re: [gmx-users] How to solve the terminal oxygen atom issue (OXT atom) ?

On 12/15/16 4:27 AM, Seera Suryanarayana wrote: Dear gromacs users, I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I

[gmx-users] constraint

GMX Users: When I run grompp on Polyetylene Oxide in water, I get the following Note: NOTE 2 [file topol-trappeR-B.top, line 423]: The bond in molecule-type PEO between atoms 2 O12 and 3 C23 has an estimated oscillational period of 6.0e-03 ps, which is less than 10 times the time step of 1.

[gmx-users] CG Lincs errors

Hi all, I¹m hoping for some help. I¹m very sorry, this is a bit of a long one. I¹ve been struggling for almost a month trying to run a CG representation of our all-atom model of a collagen protein (3 polypeptide chains in a protein). Our original AMBER all-atom model had been successful modelling

[gmx-users] How to solve the terminal oxygen atom issue (OXT atom) ?

Dear gromacs users, I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field. When I executed the pdb2gmx I got following error. Fata