[gmx-users] Failed to lock: md.log. No locks available.

Hi, Failed to lock: md.log. No locks available. still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620)

Re: [gmx-users] System blows up

Dear List and Mark I followed your suggestions equilibrating the proteins of my complex separately. In both cases i'm able to correctly equilibrate the system and to perform a short md of 500ps. So I suppose that when i simulate both protein together somewhere there is a clash. Now how could I

[gmx-users] beads in martini corse-grained

Dear Prof. I don't know about definition of sulfuric acid in Martini Corse-Grained, May I ask you to help me, Please? And Please say me about my definition of aniline as SC4, SC4, SNd that is correct? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Failed to lock: md.log. No locks available.

On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the

[gmx-users] (no subject)

Hi all, I am new to the Gromacs and just started to use Gromacs for MD simulations. I am tring to extend the simulation (protein in a box) 10 ns more. For this, I used the following command: grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o md_second.tpr mdrun It seems to run.. I

Re: [gmx-users] Failed to lock: md.log. No locks available.

On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system,

Re: [gmx-users] Failed to lock: md.log. No locks available.

There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject:

[gmx-users] Constructing covalent bond between protein-ligand complex

Dear all, Guided by gmxusers' list I have used gmx_top_tools.tgz (http://www.gromacs.org/Downloads/User_contributions/Other_software) to prepare the protein-ligand complex linked by a covalent bond. Unfortunately the tool renumtop is detecting a duplicate atom but not updating its number. Only

Re: [gmx-users] Failed to lock: md.log. No locks available.

On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li ljg...@yahoo.com.sg wrote: There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo I tried, not work. Thanks, From: lina lina.lastn...@gmail.com To:

[gmx-users] 1-4 Scaling problem of ASN-NAG from GLYCAM

Dear All, The protein on which I am working, have few ASN residues which are N-linked with the N-acetyl-glucosamine (NAG). I have taken the parameters of the NAG and N-linked ASN from the GLYCAM_06. I have added this N-linked ASN as a new residue in aminoacids.rtp file and accordingly all the

[gmx-users] pdb2gmx -ss option

Dear all, I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein. But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but

[gmx-users] Coarse-graining and cut-offs

Dear all, first of all, sorry to this rather conceptional question, which is not totally to GROMOACS related. But probably anyone of you can help. In my simulations I use mesitylene as a solvent. In future i want to coarse-grain the full atomic mesitylene to an effective one-particle. For

[gmx-users] Umbrella Sampling application

Dear Gmx Users! I do protein-ligand simulations and I am interested in binding free energy. My ligand is not charged molecule, there is no specific binding so hydrogen bonding and hydrophobic interactions are responisble for binding. I have experimental data from ITC of binding free energy. I am

Antw: [gmx-users] Coarse-graining and cut-offs

Hi Thomas, Wouldn't it be an idea to smooth this tabulated potential within some range down to zero (1.0-1.4). One could use a simple single-exponential decay in a switch-function manner. Just one suggestion and maybe not your solution. Bests, Emanuel Thomas Schlesier schl...@uni-mainz.de

[gmx-users] About spacing in umbrella sampling

Dear justin, Thanks for your previous reply which one is reliable  to get desired spacing in umbrella sampling either from output of  g_dist or from  pullx.xvg? If i choose spacing from pullx.xvg will it affect the result ? (poor  sampling and poor free energy calculation). Thanks in

Re: [gmx-users] About spacing in umbrella sampling

vidhya sankar wrote: Dear justin, Thanks for your previous reply which one is reliable to get desired spacing in umbrella sampling either from output of g_dist or from pullx.xvg? They should be equivalent. If i choose spacing from pullx.xvg will it affect the result ? (poor

[gmx-users] average force on solute

Hi,   I am simulating a peptide in a box of water in gromacs 4.5.4 . From the trajectory, I want to compute the time-averaged force acting on the peptide.  I found g_traj tool can provide information on force upon supplying the traj.trr file  and g_traj help menu also suggests that using -af