[gmx-users] protein topology file with some substitutions by other founction groups

substituted by -SH group to form a disulphur bond. So, Is there any one who can teach me how to get a topology file of a protein like this? Thank you in advance. Best Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University No.826 Zhang Heng Rd. Shanghai, China, 200032 Tel

Re:Re: [gmx-users] How to calculate PMF after AFM pulling

could simply integrate that to get the PMF. However, actually, i don't know how i can get the average force as a function of position and apply them in the PMF calculation. Could you give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan Unive

Re: [gmx-users] How to calculate PMF after AFM pulling

Hello, Justin As the mannul said, it is intended to analyze .pdo files generated by mdrun using umbrella sampling tocreate a potential of mean force (PMF). But i were using AFM method not umbrella sampling. How can i do that? Thanks. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy

[gmx-users] How to calculate PMF after AFM pulling

Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 1

[gmx-users] Re:problem in DMPC lipid bilayer

Hi, You should include the topology file of DMPC in your current directory. The present version of Gromacs seems not include the DMPC in their database. Good luck -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai

[gmx-users] Re:how to get the the force plot after pulling

> Date: Thu, 19 Mar 2009 13:52:09 +0800 > From: huifang liu > Subject: [gmx-users] how to get the the force plot after pulling > dynamic simulation using GMX-3.3 > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859

[gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3

I am recently doing a SMD. I think i did it very well. But i don't know how to get the force plot. Is there some one can give me a suggestion? Thank you very much. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)542374

[gmx-users] problem with pull direction

Hello gmx-users, I find the pulling direction in PULL INFO section of the log file is not coincident with the afm_dir1 parameter i defined in the pull.ppa. could some one tell me which direction is actually used in the pulling process? Thank you very much. Huifang Liu -- Huifang Liu (Ph.D

[gmx-users] problems with pulling direction and the initial spring position

rrect options of afm_dir1 and afm_init1? Thank you very much! Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)542

[gmx-users] Problems with SMD using gromacs

r you attention. Hope for your reply Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)542

[gmx-users] Re:problem with mdrun in parallel

? By the way, I am sorry that i made a mistake. My workstation has two 4-cords CPU, not two 8-cords CPU. Huifang. -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E

[gmx-users] problem with mdrun in parallel

10: p4_error: net_recv read, errno = : 104 In addition, it runs very well, when i use '-np 5' Hope for your help. Thanks Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Ce

[gmx-users] how to use gromacs for steered molecular dynamics(SMD)

Hi, gmx-users i want to use gromacs to pull a small ligand through a protein channel and study the interaction between the ligand and the protein during this process. However, i have not found out any useful information about steered molecular dynamics(SMD) using Gromacs software. What are the di

[gmx-users] Problems with molecular dynamic investigation of an cyclic peptide nanotube

Hi, Gromacs users, I was caught by a big problem with molecular dynamic investigation of an cyclic peptide nanotube. When i do energy minimization with em.mdp parameter file as follows, it gave out a warning: Warning: 1-4 interaction between 135 and 144 at distance larger than 1 nm. I ignored it a

[gmx-users] problem with mpirun

Hi, Gromacs users, This command "grompp_ompi -np 6 -f pr_10_200.mdp -c after_em_newton_1000.gro -p all.top -o pr_10_100.tpr -po mdrun_pr_10_100.mdp" run normally. But when i run the next command "mpirun -np 6 mdrun_ompi -s pr_10_100.tpr -c after_pr_10_100.gro -o after_pr_10_100.trr -e after_pr

[gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr

I typed this command: grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_em.tpr It responded to me like this:Invalid command line argument: speptide_empdb.tpr I am a new -learner.Can you tell me where the problem is. Thanks. ___ gmx-user

[gmx-users] Relationship between the spetide.gro file and the #spetide.gro.1#?

Hi, I am a new learner of Gromacs.I want to kown what relationship between the spetide.gro file and the #spetide.gro.1# file is and how to see the content of the #spetide.gro.1# file. Hope to get your help! ___ gmx-users mailing listgmx-users@gromacs