[gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread aiswarya pawar
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap

[gmx-users] All-bonds vs h-bonds contraints

2012-02-09 Thread gpat
Hello Could you please clarify what is the reason for adopting the "all-bonds" constraints as a standard practice in gmx protein simulations? I mean, the argument that "the time step in molecular simulations can be increased by a factor of 4 by replacing the bond vibrations by holonomic constrain

[gmx-users] how to get the block averaged MSD curve ?

2012-02-09 Thread Kiwoong Kim
Hi, I have a simulation result from 0 to 50ns after equilibration run. I want to divide this data set equally into 10blocks (10ns each) and get block averaged MSD curve (average of 10 blocks). It seems that I mange to get block MSD data by using g_msd -beginfit 0 -endfit 10, g_msd -beginfit 10 -

[gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread rarora
Dear Gromacs users, I have been trying to simulate a Protein-DNA complex using gromacs, but each time I have been facing problems. I would like to point out that both the Protein and DNA have been modeled and after that docked in order to obtain a complex. Following are the parameters I am

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread lina
On Thu, Feb 9, 2012 at 8:44 PM, wrote: > Dear Gromacs users, > > I have been trying to simulate a Protein-DNA complex using gromacs, but each > time I have been facing problems. I would like to point out that both the > Protein and DNA have been modeled and after that docked in order to obtain a

Re: [gmx-users] how to get the block averaged MSD curve ?

2012-02-09 Thread lina
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim wrote: > Hi, > > I have a simulation result from 0 to 50ns after equilibration run. > I want to divide this data set equally into 10blocks (10ns each) and get > block averaged MSD curve (average of 10 blocks). I would try some external software. excel.

Re: [gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread lina
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote: > > Dear Gromacs users, > > I have a MD simulated protein and i take frame from this and remove water > and add water implicit in the interface and want to do energy minimization > but while doing the minimization i get errors. The steps follow

[gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread aiswarya pawar
Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps followed are- pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap

Re: [gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread Justin A. Lemkul
lina wrote: On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar wrote: Dear Gromacs users, I have a MD simulated protein and i take frame from this and remove water and add water implicit in the interface and want to do energy minimization but while doing the minimization i get errors. The steps

Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

2012-02-09 Thread Justin A. Lemkul
vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of "Methane in 1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread rarora
Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NVT. I was so engrossed in other details that I forgot to mention it! Quoting lina : On Thu, Feb 9, 2012 at 8:44 PM, wrote: Dear Gromacs users, I have be

Re: [gmx-users] Error energy minimization on protein with implicit water

2012-02-09 Thread aiswarya pawar
By setting the emtol to 1.0, didnt work. Anyother way i could figure out. On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul wrote: > > > lina wrote: > >> On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar >> wrote: >> >>> Dear Gromacs users, >>> >>> I have a MD simulated protein and i take frame fro

[gmx-users] Energy minimization Error

2012-02-09 Thread francesca vitalini
Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize t

Re: [gmx-users] Energy minimization Error

2012-02-09 Thread Justin A. Lemkul
francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. The

Re: [gmx-users] Using groups in the mdp file

2012-02-09 Thread Ignacio Fernández Galván
--- On Mon, 6/2/12, Ignacio Fernández Galván wrote: > The .gro file does not contain any mention to "ACX", but I > believe it's not needed, as long as it's in the .top, > right? It seems that default group names are generated not from moleculetype names, but from residue names. At least that's

Re: [gmx-users] Energy minimization Error

2012-02-09 Thread francesca vitalini
Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? 2012/2/9 Justin A. Lemkul > > > francesca vitalini wrote: > >> Hi all! >> I'm trying to run some energy minimization with gromacs 3.3.1

[gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model

2012-02-09 Thread GZ Zhang
Hi, ALL We are writing our own MD program to simulate water and the TIP4P model is being considered. I am wondering that how does GROMACS program handle the force on the massless M site of the TIP4P model? It would be better to be informed the algorithm(or the code in GROMACS). Thanks. Gu

Re: [gmx-users] Energy minimization Error

2012-02-09 Thread Justin A. Lemkul
francesca vitalini wrote: Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? What is the Fmax you achieve, and what are your intents for this process? Minimizing very low is only

[gmx-users] Equilibration of polymer chains- gauche defects

2012-02-09 Thread Elisabeth
Hi all, Can you please guide me how one can calculate fraction of gauche+ and gauche- defects in the center of a polymer chain? Appreciate you help. Juliete -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

[gmx-users] Re: REMD tutorial

2012-02-09 Thread bharat gupta
Hi, I am planning to carry out a REMD study on a 12 residue beta-hairpin peptide. I have read the gromacs tutorial for that . I have certain doubts regarding the tutorial :- 1. Step. 4 says that "run short simulations to have an estimate of the exchange rate (can get a good estimate within ~100 p

Re: [gmx-users] Problem with simulation of Protein-DNA complex

2012-02-09 Thread Tsjerk Wassenaar
Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NV

Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

2012-02-09 Thread vivek sharma
Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished

[gmx-users] Check out my photos on Facebook

2012-02-09 Thread Wara Ell Boon
Hi Wara, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Wara To sign up for Facebook, follow the link below: http://w

Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation

2012-02-09 Thread Mark Abraham
On 10/02/2012 4:41 PM, vivek sharma wrote: Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrine

Re: [gmx-users] Re: REMD tutorial

2012-02-09 Thread Mark Abraham
On 10/02/2012 1:20 PM, bharat gupta wrote: Hi, I am planning to carry out a REMD study on a 12 residue beta-hairpin peptide. I have read the gromacs tutorial for that . I have certain doubts regarding the tutorial :- 1. Step. 4 says that "run short simulations to have an estimate of the exc

Re: [gmx-users] how does gromacs handle the force on the virtual site of the TIP4P model

2012-02-09 Thread Mark Abraham
On 10/02/2012 5:11 AM, GZ Zhang wrote: Hi, ALL We are writing our own MD program to simulate water and the TIP4P model is being considered. I am wondering that how does GROMACS program handle the force on the massless M site of the TIP4P model? It would be better to be informed the algorit