[gmx-users] Re: gmx-users Digest, Vol 79, Issue 167

Hi Tom. Hi, You show differences when using GROMACS 4.5.3 for one simulation with the pdb2gmx option -nochargegrp and one without this option (is this correct, or did you manually edit the topology to have the old charge groups?). This pdb2gmx option should have no effect in 4.5.3 as all

Re: [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167

OK that makes things clearer. As I mentioned I would check that it is not an issue with using CHARMM from 4.0.5 as if I remember correctly the CHARMM forcefield was not fully supported until version 4.5 (and I think was removed from the GROMACS 4.0.7 release so people didn't use it). As I also

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi Carsten, Thanks for your suggestion! But because my simulation will be run for about 200ns, 10ns per day(24 hours is the maximum duration for one single job on the Cluster I am using), which will generate about 20 trajectories! Can anyone find the reason causing such error? regards, Baofu

[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find

Re: [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

To see if the problem is force-field related, you could try to run the same simulations using amber-ff. If you will find the same results, probably is a software bug. Maybe the bug has been introduced in the version 4 when the Domain Decomposition has been introduced. You can check if it is a

[gmx-users] Phosphorylated Serine in charmm

Hello all, I am using charmm ff in Gromacs 4.5.2, everything goes right with standard proteins, but now i want to run a simulation on a protein with a phosphorylated residue. As mentionned in this post http://www.mail-archive.com/gmx-users@gromacs.org/msg35532.html, I changed the rtp and hbd to

[gmx-users] system is exploding

Dear gromacs users, I am trying to run simulations for small molecules in water. Topology files I created by my self for charm ff. When I am trying to start energy minimization I got an error: Steepest Descents: Tolerance (Fmax) = 1.0e+00 Number of steps = 1000 That's means my system

Re: [gmx-users] system is exploding

Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water? On 11/26/2010 11:26 AM, Olga Ivchenko wrote: Dear gromacs users, I am trying to run simulations for small molecules in water. Topology

Re: [gmx-users] system is exploding

I tried today to run minimization in vacuum for my small molecules. This has the same error. 2010/11/26 Baofu Qiao qia...@gmail.com Have you run the energy minimization (or further simulation to optimize the structure and test the FF) on the small molecule before you added it into water?

Re: [gmx-users] heme

Hi Erik I am using ffG43a1 force field. It has heme topology. But in Cyt C. FE is bonded to both NR of HIS and SD of MET. The parameter for the bond, FE SD, angles e.g. NR (HIS) FE SD(MET) and dihedral angle CH2(MET) SD (MET) FE NR(HIS) is missing in this force field. hence I am getting error

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3) Neither of 4.5.1, 4.5.2 and 4.5.3 works

Hi all, I just made some tests by using gmx 4.5.1, 4.5.2 and 4.5.3. Neither of them works on the continuation. --- Program mdrun, VERSION 4.5.1 Source code file: checkpoint.c, line: 1727 Fatal error: Failed to lock: pre.log. Already running

[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find

Re: [gmx-users] system is exploding

check your custom topology (this is where the error is 99% of the time), use qm minimized starting structures, make sure your structure matches your topology (atom names,numbers,ordering, etc.), test single molecules in vacuum first and/or reduce the step size of your SD minimizer. On

Re: [gmx-users] system is exploding

Quoting Baofu Qiao qia...@gmail.com: If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it. For simple molecules in water, there is no need for a complicated program like packmol. Such a configuration can easily be built in Gromacs.

[gmx-users] [Fwd: charge group radii]

---BeginMessage--- Hi all, I have recently been testing out the new version of Gromacs. To do so I have used files from previous simulations in Gromacs-4.0.7. When feeding the three files (mdp,gro, and top) into grompp, the following note is displayed: NOTE 3 [file pbc.mdp]: The sum of the

[gmx-users] Error while using forcefield GROMOS 43a1p

Dear Justin, I am trying to do simulation of a system which contains phosphorylated serine using GROMOS 43a1p forcefield. While running pdb2gmx command, I am getting following error. Fatal error: Atom N not found in residue seq.nr. 1 while adding improper thank you in anticipation. With

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Baofu, what operating system are you using? On what file system do you try to store the log file? The error (should) mean that the file system you use doesn't support locking of files. Try to store the log file on some other file system. If you want you can still store the (large) trajectory

[gmx-users] PR

I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water model. Is it likely mean that position restrained dynamics is not required. If we are not intersted in position restrained dynamics then what are the criteria for system needed. -- Pawan -- gmx-users mailing list

Re: [gmx-users] PR

Quoting pawan raghav pwnr...@gmail.com: I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water model. Is it likely mean that position restrained dynamics is not required. As soon as you introduce a protein or anything else, this is no longer true. If we are not intersted in

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: Baofu, what operating

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi Baofu, could you provide more information about the file system? The command mount provides the file system used. If it is a network-file-system than the operating system and file system used on the file server is also of interest. Roland On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=620) /dev/md0 on /boot type ext3 (rw) tmpfs on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type

Re: [gmx-users] Thermostat for REMD simulations in implicit solvent

Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t = 0.0109 rather than 91. Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com: Dear all,

Re: [gmx-users] Thermostat for REMD simulations in implicit solvent

I also noticed this error on my setup, so I changed tau-t to 0.1, which is commonly found on others setup. tau-t = 0.0109 seems too low. 2010/11/26 Per Larsson per.lars...@sbc.su.se Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 To make things short. The used file system is lustre. /Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: Hi Roland, The output of mount is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw)

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED

Hi all, What Roland said is right! the lustre system causes the problem of lock. Now I copy all the files to a folder of /tmp, then run the continuation. It works! Thanks! regards, $于 2010-11-26 22:53, Florian Dommert 写道: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 To make things

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED

Hi, we use Lustre too and it doesn't cause any problem. I found this message on the Lustre list: http://lists.lustre.org/pipermail/lustre-discuss/2008-May/007366.html And according to your mount output, lustre on your machine is not mounted with the flock or localflock option. This seems to be

[gmx-users] Re: displacement of drug molecule

I am CC'ing the gmx-users list, as I did on the previous message, so please continue the discussion there. sagar barage wrote: Dear sir, As per your suggestion i have design position restrain file for drug but the displacement is occur during position restrained MD plz give me any

Re: [gmx-users] free energy perturbation

antonio wrote: Dear gromacs users I am trying to carry out a free energy perturbation to evaluate the difference in binding energy between two inhibitors of the same protein. I have read a lot of post but i did no understand how to create the topology file. have i to write a mixed pdb of the

Re: [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

Francesco Oteri wrote: To see if the problem is force-field related, you could try to run the same simulations using amber-ff. If you will find the same results, probably is a software bug. Some Amber parameter sets (Amber94, I think) have issues of being overly helix-friendly, but

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Anirban Ghosh wrote: Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma

Re: [gmx-users] Phosphorylated Serine in charmm

Yasmine Chebaro wrote: Hello all, I am using charmm ff in Gromacs 4.5.2, everything goes right with standard proteins, but now i want to run a simulation on a protein with a phosphorylated residue. As mentionned in this post http://www.mail-archive.com/gmx-users@gromacs.org/msg35532.html, I

Re: [gmx-users] Error while using forcefield GROMOS 43a1p

Jignesh Patel wrote: Dear Justin, I am trying to do simulation of a system which contains phosphorylated serine using GROMOS 43a1p forcefield. While running pdb2gmx command, I am getting following error. Fatal error: Atom N not found in residue seq.nr http://seq.nr. 1 while adding

Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero

Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again.