[gmx-users] Regarding MKTOP

Dear all, I have been using MKTOP for generating topologies for Amber and OPLSAA ff. I was trying to generate CCL4 topology in both OPLSAA and AMBER ff but Its not identifing the chlorine atoms and hence it couldn't generate bond stretching, bending parametrs. Please help sort this

[gmx-users] Segmentation fault

Hi When i perform mdrun for energy minimization, I found an error revealed segmentation fault. Please explain me -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] error in Solvation

Dear Sir, The following error was found during the ions solvation even though the included water topology. #include gromos43a1.ff/spce.itp Program genion, VERSION 4.5.1 Source code file: gmx_genion.c, line: 284 Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of

[gmx-users] Simulation of a crystal

Hi to everybody!!!I'd like to know if it is possible to simulate with gromacs a crystal lattice where the atoms are just kept almost fixed in their crystallographic structure positions and they are allowed just to vibrate around this positions. This is not a real MD simulation but I need it

[gmx-users] Re: topology error

only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also.

Re: [gmx-users] Ligand scattered out of the protein

On 7/10/2011 9:18 PM, ITHAYARAJA wrote: Dear Sir, I am doing simulation work with protein-ligand complex (3 ligands). I modeled the protein using modeller, their ligand (two) was translated from the template and one them were docked by autodock 4.2. The protein and ligand coordinates were

Re: [gmx-users] snap shot

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. trjconv use -dt 5000 I don't want to save snap shot for

[gmx-users] Re: Question about Justin's Free Energy Tutorial

Thank you guys for your help. I appreciate it. On Thu, Oct 6, 2011 at 1:05 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello Justin, I have a question about your tutorial.  If I want to mutate one small group of a molecule, I would have to not provide 'couple_lambda0' and

Re: [gmx-users] Simulation of a crystal

Hi Valentina, Check position_restraints (chapter 5). These are used in standard MD during equilibration, so you can check any tutorial protocol on how to use them. Hope it helps, Tsjekr On Mon, Oct 10, 2011 at 9:22 AM, auryn_vale...@libero.it auryn_vale...@libero.it wrote: Hi to everybody!!!

Re: [gmx-users] Simulation of a crystal

Hi, You can use positional restrained, this will introduce some harmonic force which will retain the atoms to a specific position. Itamar. On 10/10/2011, at 6:22 PM, auryn_vale...@libero.it wrote: Hi to everybody!!! I'd like to know if it is possible to simulate with gromacs a crystal

Re: [gmx-users] grompp error

Mark Abraham wrote: ; water topology #include tip3p.itp grompp is not detecting the change of [moleculetype], so you will have to look at the contents of that tip3p.itp and see why. I think you will need to #include some standard force field to get the water parameters. Put the #include

[gmx-users] A quick Q: How to get the history in make_ndx

Hi, How do I use the history input in the make_ndx prompt, such as before I input name 32 A2 name 33 A3 up arrow showed me: ^[[A Alt+up arrow showed me: ^[[1;3A Just curious, Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] g_hbond

Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen

[gmx-users] g_dipoles with net charge

Dear gmx users: I am using gms 4.07, my system contains a protein with net charge and a plain,here I want to calculate the the angle between the dipoles of protein and the XY plain vs. time. What should I do? And is this way right: I define a positive center and a negative center, and define

[gmx-users] CMAP for alanine dipeptide in Charmm27 ff

I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not see any entrance referring to the cmap term in the topology file. Does this mean that Cmap won't be calculated? -- gmx-users mailing list

[gmx-users] Gromacs: Cloud Vs. Boinc Server?

Hello All, I am a poor, grad-student searching for a cheap/reliable way to perform GROMACS trypsin-dynamic simulations, and I would like to hear about other's experiences with GROMACS performance with cloud computing (i.e. Amazon's EC2 cluster compute)? Or would it be better to try to build up a

[gmx-users] error_in topology

Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the error as follows

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

which gromacs version are you using? cMAP is implemented in v4.5  or later Jianguo From: César Ávila clav...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 9 October 2011 12:07 AM Subject: [gmx-users] CMAP for alanine

Re: [gmx-users] error_in topology

balaji nagarajan wrote: Dear Users ! I have a problem in generating the topology of the attached molecule as pdb. earlier i have done using the same pdb for solvating the structure using spc and spce water box , there was no such error when i do for TIP4P and oplsaa force field i got the

R: Re: [gmx-users] Simulation of a crystal

Thank you very much...I will let you know if I can make it work ..Vale Messaggio originale Da: itamar.k...@monash.edu Data: 10/10/2011 10.37 A: auryn_vale...@libero.itauryn_vale...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users]

Re: [gmx-users] snap shot

On 8/10/2011 5:21 AM, Nilesh Dhumal wrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. So you need a suitable combination of nstxout and post-processing with trjconv. I don't want

[gmx-users] RMSF calculations

Dear all, I have a set of proteins(in pdb format) in which some are solved by X-ray diffraction and some by NMR. I have done the md simulation of these proteins using gromacs for 30ns [For NMR structures, i have taken the first model as the starting structure] Now, that i want to calculate the

Re: [gmx-users] Questions about dodecahedron box

Thanks, Tsjerk. Exactly as what you said, it was because split of molecules over the boundary. It runs smoothly right now as I started with a dodecahedron box. best, Zhenlong On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Zhenlong, I guess that some molecules

[gmx-users] FEP

Hi Gmx Users, Can you suggest some reading and some tutorial in calculations of binding free energy (ligand binding) in Gromacs? ?I want to use Free Energy Perturbation method. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] FEP

Hi Please have a look at Dr.Justin tutorial page at the following link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Cheers On Mon, Oct 10, 2011 at 12:27 PM, Steven Neumann s.neuman...@gmail.comwrote: Hi Gmx Users, Can you suggest some reading and some

[gmx-users] FEP

Hi Gmx Users, Can you suggest some reading and some tutorial in calculations of binding free energy (ligand binding) in Gromacs? ?I want to use Free Energy Perturbation method. Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

RE: [gmx-users] topology_for_3 point model

Dear Users ! Thanks for the mail , now i fixed it i have a general doubt, i saw the path of gromacs /usr/local/gromacs-4.5.3/share/top there for the three point water model only spc216.gro is there is this common for all , ie ., spc , spc/e and tip3p. Date: Mon, 10 Oct 2011

[gmx-users] Re: CMAP for alanine dipeptide in Charmm27 ff

It looks like pdb2gmx does not generate an entrance for cmap terms. I added it manually to the topology file. 2011/10/8 César Ávila clav...@gmail.com I would like to run REMD simulations on the alanine dipeptide using the Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do

RE: [gmx-users] Ligand scattered out of the protein

PBC issue? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

[gmx-users] g_hbond

Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the distance is based on Hydrogen

Re: [gmx-users] FEP

mohsen ramezanpour wrote: Hi Please have a look at Dr.Justin tutorial page at the following link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html This tutorial is not for FEP explicitly, but may be of some use. There is discussion on using the BAR

Re: [gmx-users] RMSF calculations

Hi Gurunath, Each structure in the NMR ensemble is a fit to the experimental data. Unlike an MD trajectory, you can not assume that the set of structures is a proper sample from the Boltzmann distribution, and therefore, the RMSF can not be expected to correspond to the RMSF of the system. Now,

Re: [gmx-users] g_hbond

Mr Bernard Ramos wrote: Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the online manual says that the

RE: [gmx-users] Center of mass: distance restrain for groups

Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5 pull_dim =

[gmx-users] Center of mass: distance restrain for groups

Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5 pull_dim =

Re: [gmx-users] topology_for_3 point model

balaji nagarajan wrote: Dear Users ! Thanks for the mail , now i fixed it i have a general doubt, i saw the path of gromacs /usr/local/gromacs-4.5.3/share/top there for the three point water model only spc216.gro is there is this common for all , ie ., spc , spc/e and tip3p. Please

Re: [gmx-users] Re: topology error

On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA ithayar...@gmail.com wrote: only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all

Re: [gmx-users] g_hbond

Justin A. Lemkul wrote: Mr Bernard Ramos wrote: Hi everyone! I have some questions on g_hbond. According to Manual 4.5.4, hydrogen-bonds are counted/determined by g_hbond based on angle and distance cut-offs. The distance cut-off is based on the acceptor-donor distance. However, the

Re: [gmx-users] FEP

Thank you guys! So, is there any tutorial in Gromacs for calculating free energy of ligand binding using FEP? Steven On Mon, Oct 10, 2011 at 2:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Hi Please have a look at Dr.Justin tutorial page at the following link:

Re: [gmx-users] FEP

Steven Neumann wrote: Thank you guys! So, is there any tutorial in Gromacs for calculating free energy of ligand binding using FEP? TI or BAR are better methods for calculating binding free energies, I would think. FEP is best for mutating between different species. -Justin Steven

[gmx-users] How to obtain structures with large RMSD?

Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD 0.2. I am wondering how to obtain large-RMSD structures? Thanks. -- Best, Liang Liu -- gmx-users

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD 0.2. I am wondering how to obtain large-RMSD structures? Thanks. Large

Re: [gmx-users] How to obtain structures with large RMSD?

Thanks. Will the constrain help? On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: Thanks. Will the constrain help? Bond constraints? Well, in general, they're useful, and likely necessary at high temperature to keep your system stable. Please be more specific. -Justin On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul jalem...@vt.edu

Re: [gmx-users] How to obtain structures with large RMSD?

Hey Justin, Large RMSD values would indicate non-native structures, which doesn't sound like what you're looking for.  If your goal is simply enhanced sampling, try REMD. I think this is put too boldly. There are plenty of examples where pairs from native ensembles have large RMSD: e.g.,

[gmx-users] Re: A quick Q: How to get the history in make_ndx

How do I use the history input in the make_ndx prompt, such as before I input name 32 A2 name 33 A3 up arrow showed me: ^[[A Alt+up arrow showed me: ^[[1;3A Such behavior is not programmed. You are welcome to add the necessary part of the code. CTRL+C/V solves the problem. -- Dr.

Re: [gmx-users] How to obtain structures with large RMSD?

Tsjerk Wassenaar wrote: Hey Justin, Large RMSD values would indicate non-native structures, which doesn't sound like what you're looking for. If your goal is simply enhanced sampling, try REMD. I think this is put too boldly. There are plenty of examples where pairs from native ensembles

Re: [gmx-users] How to obtain structures with large RMSD?

How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Thanks. Will the constrain help? Bond

Re: [gmx-users] How to obtain structures with large RMSD?

Hi Liang Liu, You will never get broader sampling by adding restraints. If you want to have broader sampling, raise the temperature or add denaturants. But also ask yourself the question if what you think you want is what you should be wanting. What is the actual question you're trying to solve?

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? Position restraints are inherent inhibition to structural sampling. Their intent is to prevent the protein (or whatever

Re: [gmx-users] How to obtain structures with large RMSD?

Well, I am only trying to get structures with some of them far from the initial structure (large RMSD) and some of them close to the initial one... On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Liang Liu, You will never get broader sampling by adding

Re: [gmx-users] How to obtain structures with large RMSD?

Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] FEP

FEP is a poorly defined term. It can either mean 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc), or 2) it can mean specifically computing the free energies by exponentially averaging the potential energy differences.

[gmx-users] Conference Frontiers in Biomolecular Simulation

We are proud to announce the 495. Wilhelm und Else Heraeus-Seminar Frontiers in Biomolecular Simulation to take place on Jan. 22.-25. 2012 at the Physikzentrum Bad Honnef in Germany. The conference is sponsored by the Heraeus-Foundation, Germany's premier private organisation for the advancement

[gmx-users] using gromacs with an specific GCC

Good morning, I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is that the default version of gcc in this distribution is 4.1, which is broken for Gromacs!! I can install a newer version of gcc in compatible mode with gcc 4.1, but the last one will still be the default.

[gmx-users] Virtual Sites in a polymer backbone

I wish to keep certain parts of the backbone of my polymer rigid and planar, as my primary interest is in the long length and timescale motion of the polymer. I am attempting to utilise virtual sites as a means to keep aromatic groups rigid and planar. My intention is to replace groups such as

Re: [gmx-users] Virtual Sites in a polymer backbone

Broadbent, Richard wrote: I wish to keep certain parts of the backbone of my polymer rigid and planar, as my primary interest is in the long length and timescale motion of the polymer. I am attempting to utilise virtual sites as a means to keep aromatic groups rigid and planar. My intention

Re: [gmx-users] using gromacs with an specific GCC

Nathalia Garces wrote: Good morning, I'm trying to use Scientific Linux 5.5 to run Gromacs 4.5.4. The problem is that the default version of gcc in this distribution is 4.1, which is broken for Gromacs!! I can install a newer version of gcc in compatible mode with gcc 4.1, but the last one

Re: [gmx-users] snap shot

Hello, How can I save the coordinates (in pdb or xyz format) for a particular snap shot. Nilesh On Sat, October 8, 2011 10:06 am, lina wrote: On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I

Re: [gmx-users] snap shot

Nilesh Dhumal wrote: Hello, How can I save the coordinates (in pdb or xyz format) for a particular snap shot. trjconv -dump -Justin Nilesh On Sat, October 8, 2011 10:06 am, lina wrote: On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I have a

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem for larger peptides. Cheers Cesar 2011/10/10 Jianguo Li ljg...@yahoo.com.sg which gromacs version are

Re: [gmx-users] Virtual Sites in a polymer backbone

Any particular reason why improper dihedrals would not be suitable? They are significantly easier to implement. Yes the force field parameters for the molecule are not known and I am therefore fitting the parameters to Density Functional Theory. If I allow the units to move out of plane even

Re: [gmx-users] How to obtain structures with large RMSD?

you either A) Have not been sampling long enough or B) Just might have your answer... On Oct 10, 2011, at 11:46 AM, Liu, Liang wrote: Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin.

[gmx-users] problem_with_rewritting_pdb

Dear Users ! I have minimized the attached file using the gromacs43a1 and oplsaa force field using spc water molecules I have used the following script for generating topology . i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in case of oplsaa i was able to get

[gmx-users] reasons for slow computation?

Hi all, I am doing MD simulation on two almost identical protein-ligand systems with GROMACS4.5.4 and amber99SB force fields. Almost every single parameter I used for this two systems are the same (I literally copied the mdp files for both), except that one has 65235 atoms while the other has

[gmx-users] Reduce the frequency to apply distance restrain

Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5 pull_dim = N

Re: [gmx-users] problem_with_rewritting_pdb

balaji nagarajan wrote: Dear Users ! I have minimized the attached file using the gromacs43a1 and oplsaa force field using spc water molecules I have used the following script for generating topology . i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in case of

Re: [gmx-users] reasons for slow computation?

Yun Shi wrote: Hi all, I am doing MD simulation on two almost identical protein-ligand systems with GROMACS4.5.4 and amber99SB force fields. Almost every single parameter I used for this two systems are the same (I literally copied the mdp files for both), except that one has 65235 atoms

Re: [gmx-users] Reduce the frequency to apply distance restrain

Li, Hualin wrote: Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5

[gmx-users] FEP

Hi all, I have an additional question related to what Steven Neumann was mentioning. I actually have to do a molecule mutation. I'm trying to use Michael Shirts method 1) making small changes 'alchemical' changes in the molecules and computing the free energies by any method (BAR, TI, etc).

[gmx-users] Re: reasons for slow computation?

And another difference I noticed from .log files are: .. Initial maximum inter charge-group distances: two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808 multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808 Minimum cell size due to bonded

Re: [gmx-users] FEP

So BAR is only referring to the mathematical code used to calculate the overall free energy for the FEP, correct? Yes. The information required is the same, with the exception that exponential averaging requires energy differences from only one state, whereas BAR requires energy differences

[gmx-users] not guaranteed to be binary identical ?

Hi all, I am doing my MD simulations piece by piece, with -maxh and -noappend options, so that I can link pieces of trajectories together afterward. But as I did part0001 with 48 cores, and part0002 with 72 cores, the log file told me that: #nodes mismatch, current program: 72

Re: [gmx-users] not guaranteed to be binary identical ?

Yun Shi wrote: Hi all, I am doing my MD simulations piece by piece, with -maxh and -noappend options, so that I can link pieces of trajectories together afterward. But as I did part0001 with 48 cores, and part0002 with 72 cores, the log file told me that: #nodes mismatch, current

Re: [gmx-users] Re: reasons for slow computation?

Yun Shi wrote: And another difference I noticed from .log files are: .. Initial maximum inter charge-group distances: two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808 multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808 Minimum cell size due to

[gmx-users] Re: FEP

Thanks Michael for your help. This really helps a lot. Thank you! On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hi all, I have an additional question related to what Steven Neumann was mentioning.  I actually have to do a molecule mutation.  I'm

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

After checking the topology of my peptide, I found that every term in the cMAP section involve three consecutive residues. So I guess no cMAP term is required for di-ALA.    Jianguo --- On Mon, 10/10/11, César Ávila clav...@gmail.com wrote: From: César Ávila clav...@gmail.com Subject: Re:

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

On 11/10/2011 4:51 AM, César Ávila wrote: v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file as pdb2gmx would not generate them for the alanine dipeptide. There seems to be no problem for larger peptides. Cheers Cesar That sounds like a

Re: [gmx-users] Re: reasons for slow computation?

Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. But I am still wondering that, would the difference in initial maximum inter charge-group distances (0.451 nm vs 0.450 nm) and minimum initial size of DD gird (0.620nm vs 0.618nm) make

Re: [gmx-users] Re: reasons for slow computation?

On 11/10/2011 1:40 PM, Yun Shi wrote: Hi Justin, I guess you are right, that some processors on that cluster appear to be much slower than others. More likely is that the mapping of processes to processors is faulty, as Justin said. But I am still wondering that, would the difference in

Re: [gmx-users] Re: reasons for slow computation?

Hi Yun, For comparison, the conditions have to be equal. That does not include possible hardware issues. So you should be fine. Cheers, Tsjerk On Oct 11, 2011 4:41 AM, Yun Shi yunsh...@gmail.com wrote: Hi Justin, I guess you are right, that some processors on that cluster appear to be much