Re: [gmx-users] number of coordinates does not match after POSRES

Hi Justin, Thanks for your advice. Since we are using a forcefield which could only incorporate with gromacs 3.3.1, we have no choice but to prepare the system in the old version, then run it with the latest version of gromacs. Yes, indeed the option should be with -DPOSRES instead. And the

[gmx-users] summary_distances.dat file not complete

Dear users, I ran the Perl script for Umbrella Sampling Tutorial 3, and it generated an incomplete summary_distances.dat : summary_distances.dat : 00.505 10.507 20.504 30.510 40.505 50.500 60.499 70.509 80.505 90.504 100.510 110.505 120.509 13

[gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?

Hello Users, I am planning to do a bilayer simulation with asymmetric ion concentrations using slab boundaries. I am trying to modify the concentration of each ionic species on each side of the bilayer, however, I am struggling to find a technique that will allow me to effectively manipulate the

[gmx-users] Remove all but N closest water molecules from protein

Dear Gromacs users, I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow me to create a new *.gro file containing the protein and the N closest water molecules to the protein ​, starting from a system of a solvated protein​ ? Best, Jose Borreguero -- Gromacs Users mailing

Re: [gmx-users] gmx insert-molecules

> 在 2017年6月7日，16:26，gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道： > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >

Re: [gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group

Finally I managed to find the exact syntax for the rdf calculation by adding " -ref 'com of group g1' " at the end of the command-line: gmx rdf -f cgs.gro -s cgs.tpr -o rdf.xvg -xy -ref 'com of group g1' On Thu, Jun 8, 2017 at 12:56 AM, Sajjad Kavyani wrote: >

[gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group

Dear experts, Recently I ask a question entitled "RDF of a group around CNT axis" in the mailing list in order to find proper command-line for it it turns out that the "-xy" option can help But I encounter an unusual problem therefore I decided to ask another question It turns out that the gmx

Re: [gmx-users] deltaG shifts in g_wham

On 6/7/17 4:18 PM, Alex wrote: Hi all, I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane with a narrow pore and an ion. The configurations correspond to various heights "above" the membrane (0 to 1.5 nm). In one case, the ion is K+, in another Na+. In both cases the

[gmx-users] deltaG shifts in g_wham

Hi all, I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane with a narrow pore and an ion. The configurations correspond to various heights "above" the membrane (0 to 1.5 nm). In one case, the ion is K+, in another Na+. In both cases the results are fairly reasonable, but

Re: [gmx-users] gmx insert-molecules

Please do not reply to the whole digest. On 6/7/17 2:46 PM, Shi Li wrote: On 6/7/17 1:20 PM, Li, Shi wrote: Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule

[gmx-users] Cylinder pulling through bilayer

Dear list I am attempting to pull a small molecule though a bilayer using the pull geometry cylinder with gromacs v 2016. This is the relevant portion of my mdp-file: pull = yes pull-ngroups = 2 pull-ncoords = 1 pull-coord1-groups = 1 2

Re: [gmx-users] gmx insert-molecules

> 在 2017年6月7日，13:31，gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道： > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >

Re: [gmx-users] RDF of a group around CNT axis

I noticed that the gmx rdf some how cannot find the center of mass (COM) for the CNT because after that I manually put a single particle in the COM of the CNT and calculated the rdf around it (with -xy option), the gmx rdf resulted the expected value which is a sharp peak at the radius of the cnt.

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Joao, Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab). I will try the different water models. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu,

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Just one more thing. If you're following Justin's tutorial, I guess you're using lysozyme. This protein will not deviate very much from it's crystal structure at 27ºC, let alone at -40ºC (*in the context of a molecular dynamics simulation**). I understand that it may be possible to experimentally

Re: [gmx-users] gmx insert-molecules

On 6/7/17 1:20 PM, Li, Shi wrote: Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is

[gmx-users] gmx insert-molecules

Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

​Higher complexity water models such as TIP5P and so on are able to better reproduce bulk water properties (please check the paper I linked in my earlier email). However, these models require more computational effort (due to the increased number of interactions) and may not work well in

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

On 6/7/17 12:50 PM, ZHANG Cheng wrote: Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs

Re: [gmx-users] RDF of a group around CNT axis

Dear Srinivas, That's absolutely right, I want to calculate the RDF of a certain group around the central axis of a nanotube. And as I know that the RDF of the CNT around its axis is just a sharp peak at the radius, I just tested the command-line parameters for this case, to specify that which

Re: [gmx-users] mdp options in GROMACS 4.5.5

On 6/7/17 10:05 AM, ‪Mohammad Roostaie‬ ‪ wrote: Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Hello, "spc216.gro" is not a water model, it's just a pre-equilibrated simulation box (300 K and 1 bar) with the coordinates of 216 3-site water molecules. SPC and TIP3P are two examples of 3-site water models. Water model properties are well studied and tabled (e.g.

Re: [gmx-users] RDF of a group around CNT axis

If I understand you correctly: you want to calculate the RDF of a certain group (NOT part of the nanotube) around the central axis of a nanotube? The way I do these calculations is to use the gmx trjconv tool to isolate a trajectory file of ONLY the gropus I am interested in and run my

Re: [gmx-users] mdp options in GROMACS 4.5.5

Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error. Mohammad

[gmx-users] Simulate protein at subzero condition in aqueous buffer

Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume

[gmx-users] Doubt about Normal Mode Analysis while scaling nonbonded interactions

Dear all, Is there any way of scaling the Coulombic and/or van der Waals interactions between a protein-ligand system and simultaneously doing Normal Mode analysis on the perturbed system while scaling, perhaps using free-energy code in Gromacs? Thanking in anticipation, Best Regards,

[gmx-users] RDF of a group around CNT axis

Dear experts, I want to calculate rdf of a certain group around the axis of a cnt, but I do not know what are the proper parameters to choose in the command-line. To test the parameters, I calculated the rdf of cnt itself around its axis which must be a sharp peak at the cnt radius. I tested the

Re: [gmx-users] Gromacs

On 6/7/17 8:36 AM, saranya wrote: I have already done simulation for protein and drug interacted protein complexes for 100ns. I just checked out the pressure of my system by using gmx energy command, but the calculated pressure is quite altered (20,000 pressure bar). Moreover, when I

Re: [gmx-users] mdrun with multi option

Thank you Mark. Let me explain my scenario here - Umbrella sampling simulations with 15 windows are run using -multi option to obtain PMFs. I have not noticed any issues with the output files (trr, pullf etc.) yet. I have carried out WHAM analysis using gmx wham option and obtained smooth

[gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD

Hi Group I have been trying to run a simulation that contains both 3-10 and alpha helical peptides. I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)" forcefield. Over the course of simulation, the 3-10 helix is changing to alpha as

Re: [gmx-users] number of coordinates does not match after POSRES

Hi Mark, I think I solved the problem. It should be DPOSRES instead of POSRES. The define command should be implemented as "define = -DPOSRES". Finally, the chainX_porse.itp should be included in the master topology file, not chainX-pace.top. Thanks again by the way. Simon 2017-06-07 19:18

Re: [gmx-users] RMSD analysis

On 6/6/17 4:01 PM, RAHUL SURESH wrote: Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? RMSD may be an indicator of something going on but by

Re: [gmx-users] number of coordinates does not match after POSRES

On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote: Hi Mark, Thanks for your prompt reply. What surprises me is that a change of "define = POSRES" could cause a problem. The full output from grompp is - checking input for internal consistency... calling cpp... cpp: error: POSRES: No such file or

[gmx-users] mdrun with multi option

Dear Users, I have doubts regarding simulating multiple systems using mdrun '-multi' option. I have seen that people have used this option for replica exchange (with '-replex' option, of course) where information are exchanged between the systems. In case of different systems (such as

Re: [gmx-users] Ramachandran plot

Hi, This is why you should actually copy and paste your command lines so you don't waste your time ;-) And mine. Unless you wrote your entire system to your xtc file, your tpr has more atoms than your xtc, and thus probably some more dihedrals. Make a matching subset of your tpr using gmx

Re: [gmx-users] Ramachandran plot

Dear Mark Thank you gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg This was my command.. I didn't choose any dihedral particularly On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham wrote: > Hi, > > Sounds like your choice of dihedrals doesn't match your system.

Re: [gmx-users] Simulation of pure water

Hi, On Wed, 7 Jun 2017 06:37 G R wrote: > Dear all, > > I want to calculate the relaxation of pure water cell at room temperature > and at freezing point, monitoring its equilibration in volume and in > potential energy. I have 3 question: 1) Can I use packmol for my

Re: [gmx-users] RMSD Matrix Error

Hi, You might want to measure the autocorrelation time of RMSD from your reference structure. Then you'll have an idea how long you have to wait to make a statistically independent observation. Mark On Tue, 6 Jun 2017 08:25 Apramita Chand wrote: > Dear Mark, > Thanks

Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi, You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-) Mark On Tue, 6 Jun 2017 17:49 João Henriques wrote: > Yeah, I just checked and GMX < 4.6 does not come

Re: [gmx-users] Energy Minimisation

Hi, Please read the advice on system preparation on the GROMACS webpage. You probably have clashing atoms or missing atoms (check all the warnings!) Mark On Tue, 6 Jun 2017 20:19 Pandya, Akash wrote: > Hi all, > > I have used the steepest descent method to minimise

Re: [gmx-users] Ramachandran plot

Hi, Sounds like your choice of dihedrals doesn't match your system. How did you select them? Mark On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > Dear Users > > When I try to execute ramachandran plot analysis, I get the following note > like "Dihedral around 5809,5816

Re: [gmx-users] number of coordinates does not match after POSRES

Hi, We can't tell, because position restraints are an attribute of moleculetypes and those are hidden in your itp files and you didn't share which moleculetype grompp reported was the problem. Please copy and paste terminal output to make a useful description. You'll need to include the position

[gmx-users] Simulation of pure water

Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I

[gmx-users] number of coordinates does not match after POSRES

Hi, Initially, my topology file can run grompp with .mdp and .gro. However, after putting POSRES in my mdp, the warning "number of coordinates does not match" and there is no coordinate recognized in my topology file anymore. Therefore, the option POSRES somehow changes everything. The topology

[gmx-users] Ramachandran plot

Dear Users When I try to execute ramachandran plot analysis, I get the following note like "Dihedral around 5809,5816 not found in topology. Using mult=3" (nearly 30-40 dihedrals). What is it about? Input is just protein structure extended upto 150ns. -- *Regards,* *Rahul Suresh* *Research