Re: [gmx-users] Construction of silver nanoparticles

Thank you Justin Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Tue, Oct 13, 2015 at 7:21 PM, Justin Lemkul wrote: > > > On 10/13/15 9:45 AM, SAPNA BORAH wrote: > >> Thank you Justin. >> >> I have mailed some authors. >> >> Is there any way

Re: [gmx-users] Problems introducing TP2 phosphorylated tyrosine in charmm36 Start terminus GLY-565: GLY-NH3+ End terminus ASN-822: COO- Opening force field file /home/hkhandel/bin/gmx/gromacs5.1/shar

On 10/13/15 5:52 AM, himanshu khandelia wrote: Dear All I am using pdb2gmx to read a pdb file containing a dianionic phosphotyrosine (residue TP2 in charmm36) However, for some reason, pdb2gmx detects a c-terminus right before the residue TP2, resulting in a crash. Is TP2 a residue name

Re: [gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation

Hi, Unfortunately, that should a) never happen, b) given a), rarely happen identically for successive checkpoints, c) is even more strange if your time step is a normal ~2fs, and d) is not easy to fix. To address a-c), it would be good for you to get some feedback from the PLUMED developers

[gmx-users] Problems introducing TP2 phosphorylated tyrosine in charmm36 Start terminus GLY-565: GLY-NH3+ End terminus ASN-822: COO- Opening force field file /home/hkhandel/bin/gmx/gromacs5.1/share/gr

Dear All I am using pdb2gmx to read a pdb file containing a dianionic phosphotyrosine (residue TP2 in charmm36) However, for some reason, pdb2gmx detects a c-terminus right before the residue TP2, resulting in a crash. Is TP2 a residue name reserved for a C-terminus or something? I have checked

[gmx-users] problem with restarting from cpt and _prev.cpt file in REMD simulation

Dear GROMACS users, I am running REMD simulation with Gromacs 5.0.4 and PLUMED 2.1 for already around 200ns with many smooth restarts. Unfortunately now something went wrong because I got error that: The 6 subsystems are not compatible So I checked with gmxcheck cpt files replica 1: Last frame

[gmx-users] pbc=xy with 2 walls and verlet scheme

Hi all, I use GROMACS 5.1. With pbc = xy nwall= 2 and cutoff-scheme = group everything runs fine, however, when I switch to cutoff-scheme = verlet the simulation crashes with a floating exception. Both cases can be downloaded here

Re: [gmx-users] Gromacs GPU got hang

Hi Teguh, Unfortunately, I can't see anything out of the ordinary in these outputs and, admittedly, the library trace is what I was hoping to tell the most. I can't exclude the possibility if this being a bug - either in GROMACS or in one of the runtimes used. To test this and have a chance of

Re: [gmx-users] "The sum of the two largest charge group radii is larger than rlist"

In addition, aren't tpr's made with gromacs 5 compatible with gromacs 4? Peter On 13/10/15 14:04, Justin Lemkul wrote: > > > On 10/13/15 8:01 AM, Shima ebrahimi wrote: >> >> >> Dear users, >> >> I want to calculate binding free energy with g_mmpbsa in Gromacs 4.5 but >> my trajectory has been

Re: [gmx-users] Construction of silver nanoparticles

Thank you Justin. I have mailed some authors. Is there any way or tool present in gromacs to construct nano particles? regards, Sapna Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Mon, Oct 12, 2015 at 8:22 PM, Justin Lemkul wrote: > > >

Re: [gmx-users] "The sum of the two largest charge group radii is larger than rlist"

On 10/13/15 9:05 AM, Shima ebrahimi wrote: I didn't have any problem when I had used grompp to creat md.tpr in Gromacs 5 and this happened with older version. Did my system have a problem? Also when I changed the rlist in Gromacs 4.5.3, the error was repeated This probably just means

Re: [gmx-users] "The sum of the two largest charge group radii is larger than rlist"

On 10/13/15 8:32 AM, Peter Kroon wrote: In addition, aren't tpr's made with gromacs 5 compatible with gromacs 4? No. The .tpr format is forward-compatible, not backwards-compatible. -Justin Peter On 13/10/15 14:04, Justin Lemkul wrote: On 10/13/15 8:01 AM, Shima ebrahimi wrote:

Re: [gmx-users] Construction of silver nanoparticles

On 10/13/15 9:45 AM, SAPNA BORAH wrote: Thank you Justin. I have mailed some authors. Is there any way or tool present in gromacs to construct nano particles? No, GROMACS has no molecule building/editing capability. You can build a topology, probably using x2top, but this is not always

[gmx-users] "The sum of the two largest charge group radii is larger than rlist"

I didn't have any problem when I had used grompp to creat md.tpr in Gromacs 5 and this happened with older version. Did my system have a problem? Also when I changed the rlist in Gromacs 4.5.3, the error was repeated Regards, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] "The sum of the two largest charge group radii is larger than rlist"

Dear users, I want to calculate binding free energy with g_mmpbsa in Gromacs 4.5 but my trajectory has been run with Gromacs 5. So I should have new md.tpr compatible with old version. When I use grompp I get this error "The sum of the two largest charge group radii (14.107612) is larger than

Re: [gmx-users] "The sum of the two largest charge group radii is larger than rlist"

On 10/13/15 8:01 AM, Shima ebrahimi wrote: Dear users, I want to calculate binding free energy with g_mmpbsa in Gromacs 4.5 but my trajectory has been run with Gromacs 5. So I should have new md.tpr compatible with old version. When I use grompp I get this error "The sum of the two largest

Re: [gmx-users] Extending simulation

On 10/13/15 12:54 PM, thomas knitter wrote: Hi there,, I also tried to make the simulation picked from it left off. I typed the commands below: gmx convert-tpr -s em.tpr -extend 100 -o tpxout.tpr gmx mdrun -s tpxout.tpr -cpi em.cpt After a short while, it says job is terminated. So what do

Re: [gmx-users] can not open em.tpr file

On 10/13/15 7:28 PM, thomas knitter wrote: My input files are abc.gro, index.ndx topol.top, minim.mdp. I prepared a script to get the job running module load GROMACS/5.0.4-intel-2015A-mt # gmx grompp -f minim.mdp -c abc.gro -p topol.top -n index.ndx -o em.tpr gmx mdrun -v -deffnm em gmx

[gmx-users] Extending simulation

Dr. Lemkul, My job was terminated. In the log file, it says TERM_RUNLIMIT: job killed after reaching LSF run time limit. Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Extending simulation

On 10/13/15 7:43 PM, thomas knitter wrote: Dr. Lemkul, My job was terminated. In the log file, it says TERM_RUNLIMIT: job killed after reaching LSF run time limit. You shouldn't be running anything in a queuing system without diagnosing problems yourself first. Based on the scant

[gmx-users] can not open em.tpr file

My input files are abc.gro, index.ndx topol.top, minim.mdp. I prepared a script to get the job running module load GROMACS/5.0.4-intel-2015A-mt # gmx grompp -f minim.mdp -c abc.gro -p topol.top -n index.ndx -o em.tpr gmx mdrun -v -deffnm em gmx energy -f em.edr << EOF 9 0 EOF ## I keep getting