[gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

Hi All, I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? I was running in Ubuntu 10.04, and this is what I got:             do_dssp -f 300

Re: [gmx-users] Error while running methane in water simulation

vivek sharma wrote: Hi there, I am trying to run the free energy tutorial by David mobley mentioned at /*h**ttp://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial */ While running a test run

[gmx-users] Particle Insertion Method tpi - units and compensation of charged system

Dear all, I'm using gromacs particle insertion method (integrater = tpi) to obtain the excess chemical potential of single charged atoms. On analyzing my results, two questions occurred to me: 1. The units for \mu_excess = -k_B T log _N are given according to tpi.xvg in kJ/mol*nm^3, which is

[gmx-users] Re: Implicit solvent problems

Dear all, Thank you for giving me some hints for my problems. The problems has been solved now, the key is to adjust the gb_dielectric_offset to a smaller value like 0.05， then theminimizationgets going normally. Subsequently, the NVT goes well. Still, I don’t quite understand what role theg

Re: [gmx-users] Re: Implicit solvent problems

On 14/10/2011 12:38 AM, liaoxyi wrote: Dear all, Thank you for giving me some hints for my problems. The problems has been solved now, the key is to adjust the gb_dielectric_offset to a smaller value like 0.05, then the /minimization /gets going normally. You should use the value recommen

Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

On 13/10/2011 8:16 PM, Ahmad Randy wrote: Hi All, I understand that there were already some discussions about new DSSP exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two DSSP and do_dssp do not compatible each other? If the new DSSP requires the code in d

Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy wrote: > Hi All, > > I understand that there were already some discussions about new DSSP exec > with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that > this two DSSP and do_dssp do not compatible each other? > > I was running in Ub

[gmx-users] where are Density and Volume?

Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Thanks, Yao-- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] where are Density and Volume?

Yao Yao wrote: Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Was it an NVT simulation? If so, those terms are n

Re: [gmx-users] where are Density and Volume?

Yao Yao wrote: Hi Justin, It is NVE. Is there a consistent way I can know my D and V? Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at. editconf should have printed this somewhere along the way. -Justin T

Re: [gmx-users] where are Density and Volume?

Hi Justin, thanks, that is just initial value, no fluctuation over time. yao   From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thursday, October 13, 2011 10:24 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote: > Hi

Re: [gmx-users] where are Density and Volume?

Yao Yao wrote: Hi Justin, thanks, that is just initial value, no fluctuation over time. Right. The volume is constant, therefore the initial values of density and volume are always the same. -Justin yao *From

Re: [gmx-users] where are Density and Volume?

Hi, Justin Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run. So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work. Am I supposed to do so if I wanna simulate NVE? Thanks, Yao

Re: [gmx-users] where are Density and Volume?

Yao Yao wrote: Hi, Justin Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run. So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work. Am I supposed to do so if I wanna simulate NVE?

[gmx-users] pdb2gmx charmm topology lipid

Dear Justin, Thanks for the suggestions. > The lipids are built into the CHARMM27 implementation in Gromacs. You can > generate their topology with pdb2gmx. Run pdb2gmx on a single lipid, > convert it to an .itp file, and #include it in the topology. I separated out one lipid from the POPC bil

[gmx-users] Re: pdb2gmx charmm topology lipid

ram bio wrote: Dear Justin, Thanks for the suggestions. The lipids are built into the CHARMM27 implementation in Gromacs. You can generate their topology with pdb2gmx. Run pdb2gmx on a single lipid, convert it to an .itp file, and #include it in the topology. I separated out one lipid fr

Re: [gmx-users] where are Density and Volume?

Hi Justin, Just curious. what is inside .cpt file,is there a way I can change it in readable format? I also notice that every mdrun step I got a state.cpt and state_prev.cpt as well, any difference between the two? And using .cpt seems a little faster (a couple of hours or so) than without usin

Re: [gmx-users] where are Density and Volume?

Yao Yao wrote: Hi Justin, Just curious. what is inside .cpt file,is there a way I can change it in readable format? gmxdump I also notice that every mdrun step I got a state.cpt and state_prev.cpt as well, any difference between the two? http://www.gromacs.org/Documentation/File_Formats

[gmx-users] REMD and GBSA

Hi gromacs list, I'm about to start some REMD simulations using generalized Born solvent on a protein of about 5000 atoms. I have two questions, the first of which is about gromacs, the second more about REMD in general. (1) I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an N

[gmx-users] why the pressure fluctuated wildly during the simulation?

when i simulate in the NPT , and the parameter are set as follow, Pcoupl = Parrinello-Rahman pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 5 compressibility = 6.5e-5 ref_p

Re: [gmx-users] why the pressure fluctuated wildly during the simulation?

杜波 wrote: when i simulate in the NPT , and the parameter are set as follow, Pcoupl = Parrinello-Rahman pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 5 compressibility = 6.5e-5 ref_p