[gmx-users] restarting stopped mdrun

- Forwarded Message From: Mohana lakshmi To: gmx-users-requ...@gromacs.org Sent: Mon, 11 July, 2011 1:53:04 PM Subject: restarting stopped mdrun Dear all, I kept mdrun run for 3ns but the job stopped when it reached 1263999 steps due to system shut down. I used tpbconv command (tp

Re: [gmx-users] restarting stopped mdrun

On 11/07/2011 6:35 PM, Mohana lakshmi wrote: - Forwarded Message *From:* Mohana lakshmi *To:* gmx-users-requ...@gromacs.org *Sent:* Mon, 11 July, 2011 1:53:04 PM *Subject:* restarting stopped mdrun Dear all, I kept mdrun run for 3ns but the job stopped when it reached 1263999 steps

Re: [gmx-users] restarting stopped mdrun

extend "!=" restart In your situation, no need tpbconv, Just mdrun -deffnm md -cpi md.cpt -append On Mon, Jul 11, 2011 at 4:35 PM, Mohana lakshmi wrote: > > > - Forwarded Message > From: Mohana lakshmi > To: gmx-users-requ...@gromacs.org > Sent: Mon, 11 July, 2011 1:53:04 PM > Subj

[gmx-users] reaction rate

Dear Gromacs users, I want to ask a question about reaction rate. As in umbrella sampling one can obtain Free energy profile of a reaction. Hence Ea- activation energy is known. To calculate the reaction rate one need to use Arrheniuss equation: K=Aexp(-Ea/RT). A - is a constant which characterize

[gmx-users] R: Re: g_mindist on rhombic dodecahedron system

Dear Justin, dear all, following your suggestion I used the command: trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact -o prot_boxdodfull_mol.xtc to convert my simulations, and as you anticipated all went OK: now my trajectories are without spikes, the protein is entirely i

Re: [gmx-users] R: Re: g_mindist on rhombic dodecahedron system

Anna Marabotti wrote: Dear Justin, dear all, following your suggestion I used the command: trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact -o prot_boxdodfull_mol.xtc to convert my simulations, and as you anticipated all went OK: now my trajectories are without spikes,

[gmx-users] where is water?

Hi Friends, When I run pdb2gmx, it automatically asks which water topology should be included. Also, in the .top file the lines included are: ; Include water topology #include "gromos53a6.ff/spc.itp" However, I do not see any water molecules in the .gro file. So, was water included or not? Than

Re: [gmx-users] where is water?

Ragothaman Yennamalli wrote: Hi Friends, When I run pdb2gmx, it automatically asks which water topology should be included. Also, in the .top file the lines included are: ; Include water topology #include "gromos53a6.ff/spc.itp" However, I do not see any water molecules in the .gro file. S

Re: [gmx-users] where is water?

Thanks...Glad to realize the newer version of gromacs makes life easier. Raghu On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul wrote: > > > Ragothaman Yennamalli wrote: > >> Hi Friends, >> >> When I run pdb2gmx, it automatically asks which water topology should be >> included. Also, in the .t

[gmx-users] calcium parameters

In God we trust Hi GMX-users I want to do MD simulations of amylase which has 3 ca2+ ions by Gromacs 4.5.3 and charm22 force field. I don’t want to restraints calcium and I searched mailing list and papers for Ca+2 binding parameters in Charm22 but I only found binding parameters for ca-oxyg

[gmx-users] Running QM/MM in parallel (ORCA/GMX)

Hey there, after working through the helpful tutorials about QM/MM I now ran into a problem when it comes to run ORCA/GROMACS in parallel and I could not find anything about this in the mailing list or on the gromacs page. I can run GROMACS or ORCA in parallel and QM/MM on a single core, but no

[gmx-users] Gromacs adds much more water than tleap in Amber when solvate ?

Dear Gromacs users, I'm want to use Gromacs as the main tool in my study , since Gromacs is much faster than other MD packages. I'm trying to switch from Amber to Gromacs recently. The system I test is a RNA , contains about 2000 atom. In tleap of Amber , the command is "

[gmx-users] Implicit solvent crashes with PD

Hi All, I'm having a strange problem with some implicit solvent systems and I'm wondering if anyone's experienced the same problem or if I've stumbled upon a bug. I'm testing some methodology with a robust system (everyone's favorite, 1AKI lysozyme). Running simulations with finite cutoffs

[gmx-users] ERROR: Number of grid cells is zero

I am trying to do the NPT equilibration of a cyclic peptide in DMSO solvent BOX using all atom charm force field (ffcharmm27) on GROMACS. The NVT equilibration is working but the NPT equilibration shows the following ERROR. Back Off! I just backed up results/eq50K.log to results/#eq50K.log.1#

[gmx-users] Good method to turn off electrostatics

Hi, I am running NVE simulations of a system of 1000 water molecules. I am attempting to run analogous simulations on Gromacs 4.5.4 and also on another MD program. Once finished, I will compare the results of the two programs. It was suggested to me that to compare the results of the two progra

Re: [gmx-users] Good method to turn off electrostatics

Andrew DeYoung wrote: Hi, I am running NVE simulations of a system of 1000 water molecules. I am attempting to run analogous simulations on Gromacs 4.5.4 and also on another MD program. Once finished, I will compare the results of the two programs. It was suggested to me that to compare the

Re: [gmx-users] ERROR: Number of grid cells is zero

On 12/07/2011 5:29 AM, udaya kiran marelli wrote: I am trying to do the NPT equilibration of a cyclic peptide in DMSO solvent BOX using all atom charm force field (ffcharmm27) on GROMACS. The NVT equilibration is working but the NPT equilibration shows the following ERROR. These are sympt

[gmx-users] Representing bond coupling function form in a flexible water model

Dear GMXers, I'm trying to implementing a flexible water model in "Gordillo, M.C.; Marti, J. *J. Phys.: Condens. Matter* *2010*, *22*, 284111" using GROMACS. The intra-molecular water potential has the following form: V=D{[1-exp(-alpha*r1)]^2 + [1-exp(-alpha*r1)]^2} + k_a /2 *r3^2 + k_a*r3*(r1+r2

Re: [gmx-users] Gromacs adds much more water than tleap in Amber when solvate ?

On 12/07/2011 4:46 AM, chicago.ecnu wrote: Dear Gromacs users, I'm want to use Gromacs as the main tool in my study , since Gromacs is much faster than other MD packages. I'm trying to switch from Amber to Gromacs recently. The system I test is a RNA , contains about 2000 atom.

Re: [gmx-users] calcium parameters

On 12/07/2011 2:30 AM, Mahnam wrote: In God we trust Hi GMX-users I want to do MD simulations of amylase which has 3 ca2+ ions by Gromacs 4.5.3 and charm22 force field. I don’t want to restraints calcium and I searched mailing list and papers for Ca+2 binding parameters in C

Re: [gmx-users] Representing bond coupling function form in a flexible water model

On 12/07/2011 1:12 PM, WU Yanbin wrote: Dear GMXers, I'm trying to implementing a flexible water model in "Gordillo, M.C.; Marti, J. /J. Phys.: Condens. Matter/ *2010*, /22/, 284111" using GROMACS. The intra-molecular water potential has the following form: V=D{[1-exp(-alpha*r1)]^2 + [1-exp(-

Re: [gmx-users] Implicit solvent crashes with PD

On 12/07/2011 4:51 AM, Justin A. Lemkul wrote: Hi All, I'm having a strange problem with some implicit solvent systems and I'm wondering if anyone's experienced the same problem or if I've stumbled upon a bug. I'm testing some methodology with a robust system (everyone's favorite, 1AKI lyso

[gmx-users] viscosity

Sir, I am dealing with MD simulation of ionic-liquids.I want to calculate viscosity of this system.I am trying to do it by using Green-Kubo relation for the transport properties; it is time integral of pressure correlation function but I am stuck with how to get the pressure correlation funct

Re: [gmx-users] Implicit solvent crashes with PD

Mark Abraham wrote: On 12/07/2011 4:51 AM, Justin A. Lemkul wrote: Hi All, I'm having a strange problem with some implicit solvent systems and I'm wondering if anyone's experienced the same problem or if I've stumbled upon a bug. I'm testing some methodology with a robust system (everyon