[gmx-users] Re: the output of do_dssp

Hi, Justin Thank you for your patience. According your reply, I used trjconv to write only protein group into another file. I execute do_dssp again in group "protein"and "mainchain" respectively but still get coils more than total residues. Why? Hsin-Lin Hsin-Lin wrote: > Hi, Justin: > > T

[gmx-users] PMF in vacuum

Dear Eudes: Can you please elaborate on your description? What .mdp options are you using? What exactly do your curves look like (you can post pictures to photobucket or some other online service and link them here)? If you suspect that you are doing something wrong, then we need to under

[gmx-users] PMF in vacuum

Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the d

RE: [gmx-users] Restarting after NVT: continuation error

Justin, Thanks, Its working on Gromacs4.0.7. -- Vandana Kumari From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Tuesday, May 25, 2010 6:23 PM To: Discussion list for GROMACS users S

Re: [gmx-users] How to combine two gro files in one big file

Yan Gao wrote: Thank you Vandana and Justin, the cat command solve the problem. Regarding the removement of the unnecessary lines in the middle, is there a command that can do it automatically? or one has to make code by self? Thanks. That's a trivial exercise for a simple text editor.

Re: [gmx-users] How to combine two gro files in one big file

Thank you Vandana and Justin, the cat command solve the problem. Regarding the removement of the unnecessary lines in the middle, is there a command that can do it automatically? or one has to make code by self? Thanks. Yan On Tue, May 25, 2010 at 3:25 PM, Justin A. Lemkul wrote: > > > VANDANA

Re: [gmx-users] large sim box

- Original Message - From: Yan Gao Date: Wednesday, May 26, 2010 9:19 Subject: Re: [gmx-users] large sim box To: Discussion list for GROMACS users > Hi Mark, > > Thank you for your comments! They are very helpful. > > I still have several questions regarding your comments: > 1. Which c

Re: [gmx-users] large sim box

Hi Mark, Thank you for your comments! They are very helpful. I still have several questions regarding your comments: 1. Which constraints should I apply for 2fs stepsize? hbonds, all-bonds, h-angles, all-angles I am simulating molecules that contain carbon nanotubes and polymer chains. May I have

Re: [gmx-users] A question on execusion speed

- Original Message - From: "Justin A. Lemkul" Date: Wednesday, May 26, 2010 3:16 Subject: Re: [gmx-users] A question on execusion speed To: Discussion list for GROMACS users > > > Paymon Pirzadeh wrote: > >Hello, > >I have question regarding the execution time of a trajectory. I > use

Re: [gmx-users] How to combine two gro files in one big file

VANDANA KUMARI wrote: Hi Yan, You can do it by converting your both gro file into pdb files and concatenating both pdb files into one file . and you can convert pdb into gro using editconf steps are as follows: 1. editconf -f 1.gro -o 1.pdb 2. editconf -f 2.gro -o 2.pdb 3. cat 1.pdb 2.pd

Re: [gmx-users] Restarting after NVT: continuation error

VANDANA KUMARI wrote: Hi Amit, thanks for the reply. I am using gen_vel = no in my mdp file.but I am wondering why I am getting warning message when I am using "continuation = yes" or "continuation = no ". grompp is not recognizing continuation as parameter. Am I doing something wrong? W

RE: [gmx-users] Restarting after NVT: continuation error

Hi Amit, thanks for the reply. I am using gen_vel = no in my mdp file.but I am wondering why I am getting warning message when I am using "continuation = yes" or "continuation = no ". grompp is not recognizing continuation as parameter. Am I doing something wrong? Thanks, -- Vandana Kumari

Re: [gmx-users] Restarting after NVT: continuation error

On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI < kumar...@buckeyemail.osu.edu> wrote: > > Hello Gromacs Users, > > I am trying to make tpr file for NPT equilibration after NVT equilibration > using > > grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o > npt.tpr > > I am using

RE: [gmx-users] How to combine two gro files in one big file

Hi Yan, You can do it by converting your both gro file into pdb files and concatenating both pdb files into one file . and you can convert pdb into gro using editconf steps are as follows: 1. editconf -f 1.gro -o 1.pdb 2. editconf -f 2.gro -o 2.pdb 3. cat 1.pdb 2.pdb > both.pdb you need to de

[gmx-users] Restarting after NVT: continuation error

Hello Gromacs Users, I am trying to make tpr file for NPT equilibration after NVT equilibration using grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o npt.tpr I am using parameter " continuation = yes " in npt.mdp for restarting after NVT, but I am getting this warning ma

[gmx-users] How to combine two gro files in one big file

Hi there, I want to simulate two molecules which are identical, and one is rotated/translated from another. I have the gro file for one molecule. I tried editconf, which helped manipulate the molecule. Then I want to combine it with the original gro file, so that the two identical molecules are p

Re: [gmx-users] A question on execusion speed

Paymon Pirzadeh wrote: Hello, I have question regarding the execution time of a trajectory. I used to run my trajectory at 265K or 275K and at the end of the log file the speed was reported as e.g. 1.18 ns/day. Recently, I changed the temperature to 288K and now my simulation is not finished in

[gmx-users] A question on execusion speed

Hello, I have question regarding the execution time of a trajectory. I used to run my trajectory at 265K or 275K and at the end of the log file the speed was reported as e.g. 1.18 ns/day. Recently, I changed the temperature to 288K and now my simulation is not finished in the assigned wall time (24

Re: [gmx-users] coarse grain dynamics

ram bio wrote: Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... There are tools out there to reconstruct an atomistic representation of a CG system (see link be

Re: [gmx-users] about PRODRG

Try specifying manually the hybridization of the heavy atoms and the protonation. Best regards. Lucio Montero. Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM Cuernavaca, Morelos, 62210 El mar, 25-05-2010 a las 16:11 +0

Re: [gmx-users] coarse grain dynamics

Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson wrote: > I agree with Justin on this one. Simulations run using

Re: [gmx-users] coarse grain dynamics

I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were pe

Re: [gmx-users] coarse grain dynamics

ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general consensus thus far is you won't be able to do what you want without significant effort to reconstruct your system, and perhaps then you should question whether any tools that seek to build optimal hydrogens f

Re: [gmx-users] coarse grain dynamics

thanks, but i am using gromacs version 4.0.07 On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi wrote: > Hi, > To change between representations (atomistic <--> coarse grained), if you > are using the MARTINI FF, you can use the modified version of Gromacs 3.3, > check here: http://md.

Re: [gmx-users] coarse grain dynamics

Hi, To change between representations (atomistic <--> coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG

Re: [gmx-users] coarse grain dynamics

There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia : > Hi there! > > I never worked with coarse grain simulations, but if you used

Re: [gmx-users] coarse grain dynamics

Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to "know the hydrogen bond interactions" you need to do so

[gmx-users] Re: stepsize too small ... but potential energy negative!

Dear Justin, you are definitely true. I tested with Gromacs 4.0.7 a couple of other proteins that were correctly minimized with the same machine and the previous version of Gromacs, and both of them stopped with the neighborsearching error. Then, I found a way to switch to version 4.0.5 on the sam

[gmx-users] coarse grain dynamics

Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bondi

Re: [gmx-users] question about Gromacs4.0.7: parallel run

Hi, Justin, Thank you so much. Now it works well. Yi On Mon, May 24, 2010 at 7:59 PM, Justin A. Lemkul wrote: > > > Yi Peng wrote: > >> Hi, everyone, >> >> Recently our school upgraded the clusters for us. And they install the >> Gromacs-4.0.7 for us. Before I always used Gromacs-4.0.3, the s

Re: [gmx-users] tpr file

- Original Message - From: Carla Jamous Date: Tuesday, May 25, 2010 22:54 Subject: [gmx-users] tpr file To: Discussion list for GROMACS users > Hi everyone, > > > please I have an important question: > When I continue my simulation, I do: tpbconv -s .tpr -extend    -s .tpr >

Re: [gmx-users] tpr file

Carla Jamous wrote: Hi everyone, please I have an important question: When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr mdrun -v -s .tpr -cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log At one poin

[gmx-users] tpr file

Hi everyone, please I have an important question: When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr mdrun -v -s .tpr -cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log At one point of my simulation, I had

[gmx-users] Re: stepsize too small ... but potential energy negative!

Dear Justin, to add other elements to find a solution to this problem, I repeated all the Gromacs procedure until minimization on the file PDB I used as template to model my protein. pdb2gmx warns that 232 atoms have non-zero occupancy, it's because there are sidechains with alternative conformatio

Re: [gmx-users] about PRODRG

- Original Message - From: fancy2012 Date: Tuesday, May 25, 2010 18:43 Subject: [gmx-users] about PRODRG To: gmx-users > Dear GMX users, >  When I prepare the topology file of one small molecule using PRODRG, I find > that the generated topology file is for another molecule. The only di

Re: [gmx-users] about PRODRG

fancy2012 wrote: Dear GMX users, When I prepare the topology file of one small molecule using PRODRG, I find that the generated topology file is for another molecule. The only difference between the two molecules is that the latter one has one more double bond. How should I deal with such p

Re: [gmx-users] The components on potential energy

- Original Message - From: abdullah ahmed Date: Tuesday, May 25, 2010 18:36 Subject: [gmx-users] The components on potential energy To: gmx > Hello, >   > I would like to ask for some information about the potential energy term in > the log file after minimization. I have used the OPL

Re: [gmx-users] The components on potential energy

abdullah ahmed wrote: Hello, I would like to ask for some information about the potential energy term in the log file after minimization. I have used the OPLS-AA forcefield to conduct minimization. I understand that it is the addition of a group of energy terms (bond energy, angle, LJ ect.

Re: [gmx-users] Re: stepsize too small ... but potential energ negative!

Anna Marabotti wrote: Dear Justin, I would like to say that you were true, but it isn't! :-( I launched the minimization steps first changing in my em.mdp file the emstep from 0.1 to 0.01 as you suggested, then using directly your minim.mdp file from the lysozyme tutorial to create the .tpr: i

Re: [gmx-users] Re: the output of do_dssp

Hsin-Lin wrote: Hi, Justin: Thank you for your reply. I try to select the group, 'mainchain', when prompted, and get the quantity of coil still larger than the number of residues of my protein. Then some other elements of your system are being detected as containing relevant atoms. What ha

[gmx-users] about PRODRG

Dear GMX users, When I prepare the topology file of one small molecule using PRODRG, I find that the generated topology file is for another molecule. The only difference between the two molecules is that the latter one has one more double bond. How should I deal with such problems? Thanks very

[gmx-users] The components on potential energy

Hello, I would like to ask for some information about the potential energy term in the log file after minimization. I have used the OPLS-AA forcefield to conduct minimization. I understand that it is the addition of a group of energy terms (bond energy, angle, LJ ect..) however, I do not kno

[gmx-users] Re: stepsize too small ... but potential energ negative!

Dear Justin, I would like to say that you were true, but it isn't! :-( I launched the minimization steps first changing in my em.mdp file the emstep from 0.1 to 0.01 as you suggested, then using directly your minim.mdp file from the lysozyme tutorial to create the .tpr: integrator = stee