Re: [gmx-users] Using Gromacs on a cluster

Hello Gromacs Users, I would like to know how to run the simulation on a cluster. I have cluster in my lab with 6 nodes having 16 cpus and 4 nodes having 8 cpus. What command do I have to use all the nodes? How do I know whether cpus from all nodes are being used?? Thanks in advance for help --

Re: [gmx-users] Using Glycam forcefield and amber forcefield together

Dear Gromacs Users, I have been trying to simulate a docked complex of cellobiohydrolase with cellotriose for the past 1 week. I have derived the parameters of ellotriose from ATB server and with these parameters I am getting LINCS warning at the nvt equilibration step, which I assume is due to

Re: [gmx-users] pdb2gmx error

Hi, I have been trying to build the toplogy for cellopentoase using the newly derived parameters mentioned in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the gromacs website: http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar When I try to

Re: [gmx-users] Making separate topology file for QM atoms

Dear Gromacs Users, I am interested to know how to create a separate topology file for the QM atoms of a system. It would be of great help if somebody can explain this. For my QM system, I need to include the active site residues + ligand. -- *Best Regards* BM -- Gromacs Users mailing list *

Re: [gmx-users] Using ORCA with Gromacs

Dear Gmx Users, I am trying to run a QM-MM optimization using ORCA and Gromacs 5.1.2 version. I complied gromacs 5.1.2 with ORCA as QM-MM program. Here's the output of CMakeCache.txt file for QM package: //QM package for QM/MM. Pick one of: none, gaussian, mopac, gamess, // orca

Re: [gmx-users] Defining LA atoms in .gro file

grps= Protein_AS_5YWR > QMmethod = am1 > QMMMscheme = normal > QMbasis = sto-3g > QMcharge = 0 > QMmult = 1 > > > > the QM parameters were copied from a tutorial (

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

= sto-3g QMcharge = 0 QMmult = 1 the QM parameters were copied from a tutorial ( http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html) to test the trial run. I am using ORCA for QMMM calculations. Could you please let me know how to rectify these erro

Re: [gmx-users] Defining LA atoms in .gro file

Dear GMX Users, I am trying to perform QM/MM simulation for my system and I need to define LA for the boundary between QM and MM region. I have the boundary regions but I don't know how to add them in the gro file. Do I have to manually modify the .gro file, if that's the case, adding, them

Re: [gmx-users] sugar puckering

Dear Gmx Users, I am interested in calculating cremer-pople parameters for a trisachharide ligand from its simulation docked with a protein. I found one tool g_puckering for calculating the parameters but it was written for Gromacs version 4.0.x and I am using version 5.0.4. I am not able to

Re: [gmx-users] protein ligand simulation

ANNO_CLEANUP_ADD_content=001> > | More info > <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=25130947906_rand=499504373_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > > > > On 4/19/16 9:22 PM, bharat gupta wrote: > >> On Wed, Apr

Re: [gmx-users] Protein ligand simulation

command `gmx make_ndx -f > xxx.gro`, that's because you have not created one for it. Consult the > manual for how to use make_ndx. > > Terry > Thanks Terry. I already discussed with Justin about this problem and now I know where I was going wrong.. > > > On Wed, Apr 20, 2016

Re: [gmx-users] protein ligand simulation

On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/19/16 9:08 PM, bharat gupta wrote: > >> On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 4/19/16 9:01 PM,

Re: [gmx-users] protein ligand simulation

875792_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > | More info > <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=25130648872_rand=1182875792_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001> > > > > On 4/19/16 8:28 PM, bharat

Re: [gmx-users] protein ligand simulation

4/19/16 9:03 AM, bharat gupta wrote: > >> Dear Gmx users, >> >> I am performing a protein-ligand simulation using gromacs latest tutorial >> for 5.0.x version. As per the tutorial, I included the coordinates of the >> ligand in the complex.gro file (also updated

Re: [gmx-users] Protein ligand simulation

Dear Gmx users, I am performing a protein-ligand simulation using gromacs latest tutorial for 5.0.x version. As per the tutorial, I included the coordinates of the ligand in the complex.gro file (also updated total no. of atoms after adding ligand atoms) and updated the topology file (topol.top)

Re: [gmx-users] protein ligand simulation

Dear Gmx users, I am performing a protein-ligand simulation using gromacs latest tutorial for 5.0.x version. As per the tutorial, I included the coordinates of the ligand in the complex.gro file (also updated total no. of atoms after adding ligand atoms) and updated the topology file (topol.top)

Re: [gmx-users] Restarting crashed simulation

Hi, My simulation stopped because of power outage and I restarted it using the command: mpirun -np 32 mdrun_mpi -cpi mdrun.cpt -s mdrun.cpt It shows correctly the restarting time point, however the mdrun.log is not getting updated and I don't know how to verify whether the simulation is being

Re: [gmx-users] Making index file

Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch

Re: [gmx-users] Making index file

, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from

Re: [gmx-users] Making index file

Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com wrote: Thank you for your response. But in the gro file

Re: [gmx-users] Simulation at high temperature

Thanks .. On Wed, Jul 16, 2014 at 4:28 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi, You need to perform the NVT and NPT equilibration at 353.1 K and then use your equilibrated system for the production run. On Wed, Jul 16, 2014 at 10:55 AM, bharat gupta bharat.85.m...@gmail.com

Re: [gmx-users] Simulation at high temperature

Hi, I first simulated my protein system at 300 K. Now I want to simulate the same protein system at high temperature (353.15 K). So, do I need to perform the npt and nvt equilibration again at 353.1 K first and then the final production run ?? Will it be okay to change the temp only in the

Re: [gmx-users] Salt Bridge

Hi, I want to know the default cutoff distance g_saltbr tool uses in identifying the salt-bridges.. Regards -- Bharat -- 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

[gmx-users] Some confusion related to extending a simulation

Hi, I extended a crashed simulation using the command : mpirun -np 24 mdrun -v -s mdrun.tpr -cpi mdrun.cpt I just stopped the restarted simulation after some time and found that mdrun.log was not updated, because log file and results obtained from gmxcheck are different. Here's the last

[gmx-users] Fwd: g_kinetics

Hi, While issuing the command g_kinetics, I got an error saying that the program should be complied with GNU scientific library. Please install the library and reinstall Gromacs. Is there an option where I can compile only this tool, as rest of the other gromacs tools are working fine. Regards

Re: [gmx-users] g_kinetics

compile this tool, but you still need to configure a new GROMACS build to use libgsl before make g_kinetics can be useful. Mark On Sat, May 31, 2014 at 4:17 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, While issuing the command g_kinetics, I got an error saying that the program

Re: [gmx-users] Secondary structure not visible afterconverting from .gro to .pdb

like a bug. What GROMACS command and version produced it? Mark On May 29, 2014 6:40 AM, bharat gupta bharat.85.m...@gmail.com wrote: Thanks you all for your responses. As far the chain name is concerned, that can be worked out by a simple script. But I found another issue in the converted

Re: [gmx-users] Secondary structure not visible afterconvertingfrom .gro to .pdb

wrote: It seems like you've generated a structure that does not match the preconceptions of PyMol. What is there to solve? Mark On May 29, 2014 8:09 AM, bharat gupta bharat.85.m...@gmail.com wrote: Sorry, it was my mistake actually i opened this file in excel that's why I

Re: [gmx-users] Secondary structure not visible after converting from .gro to .pdb

Hi, I energy minimized a protein consisting 10 chains using gromacs. When I converted the structure of the protein from gro format to pdb format to visualize in Pymol, it shows only one chain in ribbon form and rest of the chains are not shown ... How to rectify this error ?? Regards -

Re: [gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

okay ,... thanks On Thu, May 29, 2014 at 10:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/28/14, 9:36 PM, bharat gupta wrote: I am not concerned about secondary structure changes. But I want to visualize the entire protein structure in ribbon form after energy minimization... When I

Re: [gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bharat gupta bharat.85.m...@gmail.com Sent: 28 May 2014 21:36 To: Discussion list for GROMACS users Subject: Re: [gmx-users

Re: [gmx-users] Secondary structure not visible afterconvertingfrom .gro to .pdb

-cleanup?tc_serial=17411327790tc_rand=1534107469utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 5/28/14, 10:04 PM, bharat gupta wrote: Here's the details of my topol.top file: #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include

Re: [gmx-users] Secondary structure not visible afterconverting from .gro to .pdb

...@maillist.sys.kth.se on behalf of bharat gupta bharat.85.m...@gmail.com Sent: 28 May 2014 21:24 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Secondary structure not visible after converting from .gro to .pdb Hi, I energy minimized a protein consisting 10 chains using

Re: [gmx-users] SImulation with urea

Hi, I have some small doubt regarding using urea in simulation. Actually, I calculated the the number of urea molecules for a particular concentration in the box. For eg., the same box if filled with water occupies 43614 molecules of water and if I need to fill molecules of urea for 1M

Re: [gmx-users] Replica Exchange Molecular Dynamics

Hi, I have posted this query two times in the forum, but got no reply. Can anybody give an advice on the following question ... I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of

Re: [gmx-users] Replica Exchange MD

Dear GMX Users, I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of required number of processors for REMD in explicit water, I am trying my luck with implicit solvent. I have come across

Re: [gmx-users] About Tutorials

Dear Vidya sankar, I think this may help you with the REMD. Here's the link for the tutorial: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B This tutorial deals with REMD and

Re: [gmx-users] Restarting a crashed run

If you have done the same mistake what I did, then you should get two files with names traj.xtc and traj.trr. These files contains the results for the restarted simulation. You can use trjconv to concatenate the new (traj.xtc)+ previous(old.xtc) files. I hope this should work for you... On Mon,

Re: [gmx-users] Dihedral PCA

Hi, I want to perform the dihedral PCA for two residues of a turn region in a protein i.e 4 dihedral angles. I have created an index file for the atoms constituting phi and psi angles for those two residues. But I don't understand what has to be written in covar file .. According to manual it