Re: [gmx-users] Wrong pressure with rigid water

Hi Mark, The problem is resolved. Previously, I was using rlist = rvdw = rcoulomb = 1.2, which leads to high pressure from NVT run. NPT equilibrated avg box length (7.13927 nm) was used for NVT run. But I got correct pressure by using rlist = rvdw = rcoulomb = 1.4 (suitable for GROMOS force

Re: [gmx-users] PBC issues with membrane-peptide simulation

Dear users, Well, I have found another solution for avoiding the diffusion through the periodic boundary in such simulations. Hope this is helpful to others doing similar work. Basically, the idea is to apply a biasing potential to the COM of the peptides to pull them towards the membrane so as

Re: [gmx-users] MD simulations of two chains protein

Hi Mark, Below, the link to the rmsf plot I had for my protein throughout 20 ns simulation. https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0 The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq rmsf.pdb -res Thank you *Khadija AMINE* *Computational Biology*

[gmx-users] Updated CHARMM36 force field files

Hi All, An updated set of CHARMM36 force field files for GROMACS is available from our website: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs There are several notable changes in this release that may be of interest to you. 1. The protein parameter set has been updated to include

Re: [gmx-users] About Area per lipids in Mixed Membranes

On 11/15/16 2:29 PM, Poncho Arvayo Zatarain wrote: Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128 lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i calculate the

Re: [gmx-users] No interaction between manually added atoms

On 11/15/16 7:44 AM, Kamps, M. wrote: Dear GMX-users, I'm experiencing difficulty with my manually added atoms to create a metallic surface within GROMACS. My goal is to create a surface (at this point metallic, Al) and let it interact with a protein. In my current situation I've only

Re: [gmx-users] Atomtype SDMSO not found - GROMACS

On 11/15/16 5:22 AM, Manasa Surakala wrote: I am new to GROMACS, running protein-ligand simulation. The error is as follows: *Fatal error:* *Atomtype SDMSO not found. * after the command: gmx grompp -f em.mdp -c solv_13948302.gro -p topol.top -o ions_13948302.tpr Can you please help me to

[gmx-users] About Area per lipids in Mixed Membranes

Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128 lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i calculate the area per lipid using (Box X * Box Y)/(#lipids per

[gmx-users] Tutorials to apply NMR data on Gromacs calculations of protein struture

Hi All, I would like to combine NMR study (specifically relaxation data, RDC and dihedral restraints) with Gromacs calculations to study possible ensembles of protein structure. I tried to search NMR refinement by Gromacs but could not see any tutorial for this purpose, except one with distance

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Issue #2077 created, thanks! On Tue, Nov 15, 2016 at 11:11 AM, Mark Abraham wrote: > Hi, > > Yes that seems a bit inconsistent. Please file a redmine and include e.g. a > tarball of suitable inputs to reproduce what's going on within grompp. > > Mark > > On Tue, Nov 15,

Re: [gmx-users] REMD ensemble of states

Hi Mark, I understand that at each replica the coordinates of the accepted states are saved. I understand that I can calculate different properties of 0.xtc in differenr programs, e.g., gromacs, MDTraj, etc., but when it comes down to visualization in VMD, for example, in gromacs I don't seem

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Yes that seems a bit inconsistent. Please file a redmine and include e.g. a tarball of suitable inputs to reproduce what's going on within grompp. Mark On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho wrote: > Hi, Mark, > > Actually, there seems to be a bug somewhere,

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Mark, Actually, there seems to be a bug somewhere, because if I defined three type 9 dihedrals in a file and then I define the same three type 9 dihedrals later on, there should be three warnings: one for each multiplicity. there were only two warnings, which means the first one somehow is

Re: [gmx-users] Wrong pressure with rigid water

Dear Mark, I have forgot to mention one point. All the data that are provided in the previous mail, are for simulation with rigid water molecules. Best regards, Sudip On Tue, Nov 15, 2016 at 7:00 PM, Sudip Das wrote: > Dear Mark, > > Sorry if I misunderstood your point.

Re: [gmx-users] Wrong pressure with rigid water

Hi, The box size changed over the NPT equilibration. You can't just use the average size if that includes the non-equilibrated times. Mark On Tue, Nov 15, 2016 at 2:30 PM Sudip Das wrote: > Dear Mark, > > Sorry if I misunderstood your point. I am aware that GROMOS force

Re: [gmx-users] Wrong pressure with rigid water

Dear Mark, Sorry if I misunderstood your point. I am aware that GROMOS force field was parametrized to work with rigid water. My aim is also not to use flexible water. I have performed the flexible water simulation just for testing purpose. Also the box length is converged (with a 0.0005 nm

Re: [gmx-users] Fwd: Error-File must be an ascii script

Thank you On Tue, 15 Nov 2016 at 5:47 PM, Mark Abraham wrote: > Hi, > > The list can't take attachments, so we can't see your script. You need to > find out how to call the mpirun you're expected to use - that's a problem > you and every other user of your cluster

[gmx-users] No interaction between manually added atoms

Dear GMX-users, I'm experiencing difficulty with my manually added atoms to create a metallic surface within GROMACS. My goal is to create a surface (at this point metallic, Al) and let it interact with a protein. In my current situation I've only modelled the aluminium surface (non-bonded

Re: [gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

Hi, Yes, probably useful, but unfortunately nobody has wanted to implement it before now. You can of course use gmx select to write out a dynamic per-frame selection of waters, and then gmx trjconv to extract frames that include velocities. That's not very efficient, but does what you seem to

Re: [gmx-users] Wrong pressure with rigid water

Hi, That's not what I suggested you need to think about. Lots of things go into making a useful physical model, and the fact that so far you think the pressure is OK is only a tiny part of that. You chose a force field that was parametrized to work with rigid water. If you use it with something

Re: [gmx-users] Wrong pressure with rigid water

Dear Mark, Thanks for your reply. As rigid water was not giving reasonable pressure, I have tried with flexible one where pressure is behaving well upto 2 ns of NVT simulation. Here is the details of my system: System: Protein in water # of residues in protein: 188 # of water molecules: 17876

Re: [gmx-users] Fwd: Error-File must be an ascii script

Hi, The list can't take attachments, so we can't see your script. You need to find out how to call the mpirun you're expected to use - that's a problem you and every other user of your cluster needs solved, so please go and ask someone who can simultaneously solve the problem for you and for

Re: [gmx-users] Error with a ligand molecule by ATB

Thank you. I solved the problem already. The file provided by ATB had a problem, and I have fixed it. 2016. 11. 15. 오후 8:13에 "Nikhil Maroli" 님이 작성: > You might need to check the atom naming in both ligand.gro and *.itp file > and correct it > -- > Gromacs Users mailing list

[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

Hi there: I am trying to analyze a water shell around a protein, and we are studing for instance deltaH in some molecular processes. In this sense as you know Enthalpies not only depend on Potential energy but also on Kinetic energies and a term pV, so that it is crutial having velocities for

Re: [gmx-users] Error with a ligand molecule by ATB

You might need to check the atom naming in both ligand.gro and *.itp file and correct it -- 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_Lists *

Re: [gmx-users] Fwd: Error-File must be an ascii script

Hi... this s my script file. And I am totally unaware of my cluster documentation On Tue, Nov 15, 2016 at 1:40 PM, Mark Abraham wrote: > Hi, > > No, because I can neither see your script nor read your documentation :-) > > Mark > > On Tue, 15 Nov 2016 09:09 RAHUL

Re: [gmx-users] Atomtype SDMSO not found - GROMACS

HI, It clearly says Atomtype SDMSO not found. Check the atomype SDMSO If it is in ligand check the .itp files -- 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

[gmx-users] Atomtype SDMSO not found - GROMACS

I am new to GROMACS, running protein-ligand simulation. The error is as follows: *Fatal error:* *Atomtype SDMSO not found. * after the command: gmx grompp -f em.mdp -c solv_13948302.gro -p topol.top -o ions_13948302.tpr Can you please help me to overcome this error? Thanks in advance, Manasa

Re: [gmx-users] Fwd: Error-File must be an ascii script

Hi, No, because I can neither see your script nor read your documentation :-) Mark On Tue, 15 Nov 2016 09:09 RAHUL SURESH wrote: > Thank you. Let me check my cluster documentation. Anyway you can help me to > correct my script? > > On Tue, 15 Nov 2016 at 1:35 PM, Mark

Re: [gmx-users] Md simulation H-atom trajectory analysis.

Hi, On Tue, 15 Nov 2016 06:26 maria khan wrote: Dear justin Thanks for your prompt response. My results are satisfactory.and i managed the H-atoms by _ignh command.but i just want to learn its solution by conventional system of gromacs also thats y i am asking.

Re: [gmx-users] Fwd: Error-File must be an ascii script

Thank you. Let me check my cluster documentation. Anyway you can help me to correct my script? On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham wrote: > Hi, > > The error message is probably exactly right - you've incorrectly specified > the required argument to mpirun

Re: [gmx-users] MD simulations of two chains protein

Hi, It's hard for anyone to know what you're doing and seeing unless you share actual command lines, and upload your resulting graphs to a file-sharing service and provide a link (the list does not take attachments) Mark On Tue, 15 Nov 2016 08:51 Khadija Amine wrote: > Ok

Re: [gmx-users] Fwd: Error-File must be an ascii script

Hi, The error message is probably exactly right - you've incorrectly specified the required argument to mpirun -np. This is not a gromacs problem - check your script and consult your cluster's documentation. Mark On Tue, 15 Nov 2016 05:59 RAHUL SURESH wrote: > I want

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Ok that makes sense. Otherwise it would have seemed like it had to be a code bug. Maybe we could add a warning for including the same file twice? Does anybody do that deliberately E.g with different preprocessor variables defined? Mark On Tue, 15 Nov 2016 00:30 Elton Carvalho