[gmx-users] energy minimization problem

Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I proceed for energy minimization I get the carbon

[gmx-users] energy minimization problem

Hi, The mdp file has pbc= xyz in the last line. In the previous mail it was written that pbc=full. Plaese ignore it. Thanks and regards Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Fatal error: The X-size of the box times triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

On 6/1/15 6:39 AM, Kevin C Chan wrote: Dear Users, I have encountered Fatal error: The X-size of the box times triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size during a pre-equilibrium (NPT) run. It is NOT an annealing process and temperature

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

Hi Dewey, maybe a little bit off topic but your description of the system reminded me of a paper I read a couple of years ago. Do you know about the ABF method and the work of Lamoureux et al? (http://pubs.acs.org/doi/abs/10.1021/ja300129x) maybe worth checking because it sounds like the

Re: [gmx-users] energy minimization problem

On 6/1/15 8:06 AM, soumadwip ghosh wrote: Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I seem to have to post this information weekly... Here is

Re: [gmx-users] energy minimization problem

On 6/1/15 9:07 AM, soumadwip ghosh wrote: Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a

Re: [gmx-users] energy minimization problem

On 6/1/15 2:28 AM, soumadwip ghosh wrote: Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I

Re: [gmx-users] confusion on NPT MD simulation

On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0

Re: [gmx-users] energy minimization problem

Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a possible way out. Regards, Soumadwip Research

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

On 5/31/15 4:17 PM, MPI wrote: Dear Users, I have a protein-lipid bilayer system and this protein is an ion channel. I would like to force a substrate eg, ammonia (NH3) passing through this channel. I wonder when it is appropriate to add NH3 into the system and how to setup the

Re: [gmx-users] energy minimization problem

Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing I am not

[gmx-users] confusion on NPT MD simulation

Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout

Re: [gmx-users] No default Ryckaert-Bell. types for proline

​Thanks Justin, I did not but I tried just now. The aforementioned dihedral terms ​remain along with the errors. Thanks in advance, Kevin On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/1/15 10:57 AM, Kevin C Chan wrote: Dear Users, I am testing with OPLSSaa

Re: [gmx-users] trjcat issue

On 6/1/15 12:05 PM, Ebert Maximilian wrote: Hi, try to set the time manually. It fixed the problem for me (-settime). The problem here isn't with trjcat, it's with subsequent calls to trjconv that specify non-existent times. -Justin Max On May 28, 2015, at 4:43 AM, Giannis Gl

[gmx-users] bend angles of a kink motif

Dear Users Can we calculate the bend angle of a kink motif in an alpha helix from a .xtc file? Thanks a lot. H.A -- 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

Re: [gmx-users] trjcat issue

Hi, try to set the time manually. It fixed the problem for me (-settime). Max On May 28, 2015, at 4:43 AM, Giannis Gl igalda...@gmail.com wrote: Dear all, I tried to concatenate two trajectories using the comand trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc

Re: [gmx-users] Volume of active site

Thanks Dr Erik , I will try your suggestion. Regards, Raja On Jun 1, 2015 8:42 PM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of g_sas -tv (gmx sas nowadays). Kind regards, Erik On

Re: [gmx-users] Constraints in the villin system

Thank you very much Justin. 2015-06-01 18:10 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 6/1/15 11:55 AM, Mario Fernández Pendás wrote: Dear all, I am interested in simulations with the villin system using the constraint algorithm SHAKE. From the physical point of view, does it make

Re: [gmx-users] Constraints in the villin system

On 6/1/15 11:55 AM, Mario Fernández Pendás wrote: Dear all, I am interested in simulations with the villin system using the constraint algorithm SHAKE. From the physical point of view, does it make any sense to perform a simulation only with the hydrogen atoms constrained? Bonds involving

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

Hi, thanks diana for your input and for the review. I never used GROMOS so far and I feel less comfortable using an unknown FF at this point. I am writing a tutorial on how to parameterize organic molecules right now and will publish it this week. Maybe you can comment on the strategy to have

Re: [gmx-users] No default Ryckaert-Bell. types for proline

pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) 1: TIP4P TIP 4-point, recommended 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) 1: PRO-ZWITTERION_COO- (only use with zwitterions containing

[gmx-users] VMD Visulazation

hello Gromacs community, I have a quite embarrassing question to ask. I couldn't find a way to visualize my gromacs trajectory in VMD. There are no tutorial online. By nature, VMD does not recognize Gromacs toplogy file. I see that on Gromacs's website there are two scrippts available:

Re: [gmx-users] VMD Visulazation

On 6/1/15 12:07 PM, Victor Ma wrote: hello Gromacs community, I have a quite embarrassing question to ask. I couldn't find a way to visualize my gromacs trajectory in VMD. There are no tutorial online. By nature, VMD does not recognize Gromacs toplogy file. I see that on Gromacs's website

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 10:57 AM, Kevin C Chan wrote: Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as

[gmx-users] Constraints in the villin system

Dear all, I am interested in simulations with the villin system using the constraint algorithm SHAKE. From the physical point of view, does it make any sense to perform a simulation only with the hydrogen atoms constrained? Otherwise, when I try to constraint all the atoms using PBC and domain

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 12:09 PM, Kevin C Chan wrote: ​Thanks Justin, I did not but I tried just now. The aforementioned dihedral terms ​remain along with the errors. Please provide your full pdb2gmx command, all screen output, and full topology. Use file sharing services, pastebin, etc. as needed.

Re: [gmx-users] Volume of active site

Thanks Dr Ebert ...looks very useful site for my purpose and I try it tomorrow when I get to the lab. Regards, Raja On Jun 1, 2015 9:52 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Raja, you could also give 3V a try: http://3vee.molmovdb.org Cheers, Max On Jun 1, 2015, at 11:12 AM,

Re: [gmx-users] Volume of active site

Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of g_sas -tv (gmx sas nowadays). Kind regards, Erik On 1 Jun 2015, at 15:19, Raj D gromacs.fo...@gmail.com wrote: Dear user, I have completed a set of MD simulations of mutants and wild

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

I wonder when it is appropriate to add NH3 into the system and how to setup the control of temperature coupling in thermostats. For example, 1. add NH3 first with the protein and then embed protein-NH3 into the lipid or 2. embed the protein into lipid with an equilibration,

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

On 6/1/15 12:13 PM, MPI wrote: I wonder when it is appropriate to add NH3 into the system and how to setup the control of temperature coupling in thermostats. For example, 1. add NH3 first with the protein and then embed protein-NH3 into the lipid or 2. embed the protein into lipid

Re: [gmx-users] Volume of active site

Hi Raja, you could also give 3V a try: http://3vee.molmovdb.org Cheers, Max On Jun 1, 2015, at 11:12 AM, Erik Marklund erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk wrote: Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of

[gmx-users] Volume of active site

Dear user, I have completed a set of MD simulations of mutants and wild type of a protein complexed with its substrate in its active site , I have inferred that the active sites of all mutant enzymes have gone enlarged relative to wild type which is consistent with our kinetic study of the

[gmx-users] No default Ryckaert-Bell. types for proline

Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as follows: ERROR 1 [file topol.top, line 161]:

Re: [gmx-users] Adding a substrate into protein-lipid bilayer system

On 6/1/15 10:18 AM, MPI wrote: Hi Justin, Thank you very much for your suggestion. Please see below. Thanks, Dewey I wonder when it is appropriate to add NH3 into the system and how to setup the control of temperature coupling in thermostats. For example, 1. add NH3 first with the

[gmx-users] new box types

Dear all, in editconf, we define boxtype using -bt, and the options we mainly use are triclinic, cubic, dodecahedron or octahedron. How to specify other types, like cylindrical, hexagonal etc? Regards, BP. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] VMD Visulazation

Hello Justin, Thanks a lot for the quick response. So I first load the .gro file from the previous step which is my initial coordinate file, I then loaded the .trr file. But I am getting some wired image. Please see attachment. Thank you. Victor -- Gromacs Users mailing list * Please search

Re: [gmx-users] VMD Visulazation

Hey Victor, check http://manual.gromacs.org/current/programs/gmx-trjconv.html you probably need -ur and -pbc Cheers, Max On Jun 1, 2015, at 1:45 PM, Victor Ma victordsmag...@gmail.commailto:victordsmag...@gmail.com wrote: Hello Justin, Thanks a lot for the quick response. So I first load

Re: [gmx-users] new box types

Hi, You can only specify a box that can be represented as a triclinic cell, and not all kinds of periodicity are supported, either. Mark On Mon, Jun 1, 2015 at 8:41 PM B P 4grom...@gmail.com wrote: Dear all, in editconf, we define boxtype using -bt, and the options we mainly use are

[gmx-users] g_rdf: normalize by density

Hi, I want to plot g_rdf for peptide and SDS. In many papers I have read *The functions were normalized by the number of atoms in the first selection (peptide atoms) and by a density of 0.01*. 1) I don''t find any option in g_rdf to normalize by density of 0.01. There is one option