[gmx-users] Spherical Position Restrain from the center of the Box

Dear gromacs user: I plan to do a coarse grain simulation for a whole virus coat. It only contains virus surface protein, so I'm afraid it will collapse due to lack of inner member lipids. I plan to add a Spherical Position Restrain from the center of the Box, to prevent the surface protein fa

[gmx-users] 答复: -extend problem

Dear gromacs users: Can anyone tell me why the total potential energy initially rises rapidly after which it relaxes again during a MD simulaiton? Thanks. Best regards, 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 gromacs query 发送时间: 20

[gmx-users] how to set number of exchange attempts in replica exchange simulation

Dear gromacs user: I recently viewed a paper which says the number of exchange attempts should be chosen to significantly exceed the transit number for for the replica-exchange scheme. But I don't know where to set the number of exchange attempts in replica exchange simulation. Can anyone help,

[gmx-users] continue a crashed run, but change the output frequency

Dear gromacs user: Is there any way to continue a crashed run, but also change the output frequence? I have tried to run a replica exchange, after run several days, I realized that the output file is too large, after the disk is full, it stop. I have backup the data, and want to continue the cr

[gmx-users] 答复: (no subject)

Thanks a lot for the help. Best regards, Haiping Zhang 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul 发送时间: 2014年6月8日 23:39 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] (no subject) On 6/8/14, 2:50 AM, #ZHANG HAIPING# wrote

[gmx-users] 答复: ligand_protein binding free energy caculation using gromacs

, 6:25 AM, #ZHANG HAIPING# wrote: > Dear gromacs user: > > Can I used gromacs to calculate the binding free energy of ligand_protein > complexes? Is there any relevant tutorial or paper? Thanks a lot. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbr

[gmx-users] (no subject)

Dear gromacs user: In the online manul it says "the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg, 0 means no ouput, should be a multiple of nstcalcenergy". But in the tutorial of free energy circulation of methane it use "nstdhdl = 10" and nstcalcenergy is

[gmx-users] ligand_protein binding free energy caculation using gromacs

Dear gromacs user: Can I used gromacs to calculate the binding free energy of ligand_protein complexes? Is there any relevant tutorial or paper? Thanks a lot. best regards, Haiping Zhang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

[gmx-users] 答复: the water box become much larger in high temporature replicas after replica exchange simulation

simulation On Jun 5, 2014 8:34 AM, "#ZHANG HAIPING#" wrote: > > Dear gromacs user： > > I have used follow .mdp to run the replica exchange simulation, after the simulation, I find the water box become much larger in high temporature replicas, can anyone tell me how to solve t

[gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation

Dear gromacs user： I have used follow .mdp to run the replica exchange simulation, after the simulation, I find the water box become much larger in high temporature replicas, can anyone tell me how to solve this? By the way, is it caused by the water box not large enough? title = repl

[gmx-users] 答复: 答复: Welcome to the "gromacs.org_gmx-users" mailing list

t; mailing list On Thu, May 29, 2014 at 11:24 AM, #ZHANG HAIPING# wrote: > Dear gromacs user: > Can any tell me how to determine the cut-off parameter e.g. rcoulomb, > rvdw in the mdp file. This should generally be determined in consultation with the literature on using the forcefiel

[gmx-users] 答复: Welcome to the "gromacs.org_gmx-users" mailing list

Dear gromacs user: Can any tell me how to determine the cut-off parameter e.g. rcoulomb, rvdw in the mdp file. By the way, how to plot a graph of strength versus distance for the 12-6 Lennard-Jones potential, Is the g_energy has such function? Thanks for you help. Looking forward you reply. Be

[gmx-users] 答复: 答复: about exchange replica with replicas 140

ues. On Thu, May 22, 2014 at 12:47 AM, #ZHANG HAIPING# wrote: > Dear Justin: > The scripts I used is as follow: > ## Set job parameters > > ## Job Name > #BSUB -J OpenMPI > > ## Queue Name > #BSUB -q medium_priority > > ## Output and Input Errors >

[gmx-users] 答复: about exchange replica with replicas 140

_ 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul 发送时间: 2014年5月22日 10:57 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] about exchange replica with replicas 140 On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: > Dear gromacs user: > > I have encounter a prob

[gmx-users] about exchange replica with replicas 140

Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used i