Re: Antw: Re: [gmx-users] calculate residence time for a protein complex

Dear Emanuel, Thank you so much for the response. I did the H bond count using the g_hbond. After this these H bond are correlated against time right?? I just want to make sure I got it right. And more over I should give a distance constrain so as to give me the existence of water at a time.

Re: [gmx-users] OPLS-AA Unknown Atomtype

Yao Yao wrote: Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error "Unknown Molecule_Atomtype". I have opened all the files in the OPLS force field but really do not see any other f

Re: [gmx-users] Free Energy Integrator Selection

Hi there, I am also doing FEP calculations and I am also using sd as integrator. The problem that I am having with this integrator is the temperature coupling (NTP). I am setting the targeted temperature of the system on 300K, for 2 Groups, Protein_and_ligand and Solvent. g_energy gives me 303

[gmx-users] Free Energy Integrator Selection

Try running for longer and look at the convergence of the temperatures over time. I suspect that what you are reporting is actually just statistical noise. I am not sure about using the sd integrator and defining multiple temperature coupling groups... If you define the same temperature for

[gmx-users] Re: pdb2gmx fatal error - atom not found

C Colenso wrote: Hi Justin, I got your email from the Gromacs mailing list...I hope you don't mind. I have a problem with pdb2gmx. I have downloaded the 4.5.4 version of gromacs, no luck, I have consulted the mailing lists and bugzillas, and tried every suggestion but this is still not fixin

[gmx-users] 答复: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

Thanks for your important advice, I am extending my simulation to 60ns, if it is still not long enough, I’ll extend another time. Thank you. 发件人: Jianguo Li [mailto:ljg...@yahoo.com.sg] 发送时间: 2011年8月22日 9:52 收件人: KONG Xian 主题: Re: Re：the mdp parameters for localpressure calculation using

[gmx-users] (no subject)

Hi what do I need for a md with gromacs? I made a tutorial in which I download an example file, but what I I don't have such a file downloaded from the pdb? What do I need to create a first input file? Greetings -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

Re: [gmx-users] (no subject)

Joschua Sterzenbach wrote: Hi what do I need for a md with gromacs? I made a tutorial in which I download an example file, but what I I don't have such a file downloaded from the pdb? What do I need to create a first input file? To run a simulation, you need coordinates (.gro,.pdb, etc)

[gmx-users] Regarding xpm2ps

Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x an

Re: [gmx-users] Regarding xpm2ps

bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example

Re: [gmx-users] OPLS-AA Unknown Atomtype

Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /s

[gmx-users] Viscosity units: Please Reply

Dear gmx-users, I have posted this question on gmx-users list few days ago 2-3 times. But I didn't receive any suggestion/reply. I have searched a lot on previous posts related to Viscosity calculations but unable to get any suitable reply. Please reply if someone has solution of following problem

Re: [gmx-users] Regarding xpm2ps

Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend lege

[gmx-users] error:You might need to add atom H to the hydrogen database of residue

Hi all,   I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error.   I have not been able to pinpoint where in the pdb file, ffamber03