[gmx-users] cutoff-scheme in CPU GPU
Hi, all Recelly I am testing the speed of GMX4.6 on our new supercomputer. There are two parameters cutoff-scheme and nstlist . for GPUs I uesd: cutoff-scheme=Verlet nstlist = 20 I found the speed is fast. I have tested if I use cutoff-scheme=Verlet combined with nstlist=20 for CPUs, the speed was pretty fast. Could I use the same parameter for CPUs? - Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] cutoff-scheme in CPU GPU
Hi, all Recelly I am testing the speed of GMX4.6 on our new supercomputer. There are two parameters cutoff-scheme and nstlist . for GPUs I uesd: cutoff-scheme=Verlet nstlist = 20 I found the speed is fast. I have tested if I use cutoff-scheme=Verlet combined with nstlist=20 for CPUs, the speed was pretty fast. Could I use the same parameter for CPUs? -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constraint error
Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move constraints ??Please help me to understand this ... Fatal error: [ file gold_bulk.itp, line 16 ]: Atom index (2) in constraints out of bounds (1-1). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. Thanks and Regards Lovika -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] binding sites with MD
Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns, movement of ligand molecules can be seen around certain sites only for both the runs. Can these sites be considered as binding sites? Also, ligand molecules are involved in both hydrophobic and hydrogen bonding interactions with these sites. Thanks in advance. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] binding sites with MD
On 5/24/14, 6:24 AM, Nidhi Katyal wrote: Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns, movement of ligand molecules can be seen around certain sites only for both the runs. Can these sites be considered as binding sites? Also, ligand molecules are involved in both hydrophobic and hydrogen bonding interactions with these sites. It's possible, but at such large ligand:protein ratios, you'll probably get a lot of nonspecific binding, and the interactions could be getting stuck in local minima, so you need some way of scoring the outcome based on energy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] constraint error
On 5/24/14, 4:46 AM, Lovika Moudgil wrote: Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move constraints ??Please help me to understand this ... Fatal error: [ file gold_bulk.itp, line 16 ]: Atom index (2) in constraints out of bounds (1-1). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. It seems that you have only 1 atom defined in the [moleculetype], but then you are defining a constraint involving atom 2, which does not exist. The error is similar to a common mistake involving positions restraints: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds If you need more specific advice, please provide us with the content of the problematic topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] constraint error
Thanks for reply Justin . Yes ...I get your point . Regards Lovika On Sat, May 24, 2014 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/24/14, 4:46 AM, Lovika Moudgil wrote: Hi everyone... Can any body help me ...As i have an .itp file in which I have defined constraint and then I am defining this .itp file in my .top fileAnd with grompp command I got this error . I think I have defined constraints on right place. Than why this error ??Where I need to move constraints ??Please help me to understand this ... Fatal error: [ file gold_bulk.itp, line 16 ]: Atom index (2) in constraints out of bounds (1-1). This probably means that you have inserted topology section constraints in a part belonging to a different molecule than you intended to. In that case move the constraints section to the right molecule. It seems that you have only 1 atom defined in the [moleculetype], but then you are defining a constraint involving atom 2, which does not exist. The error is similar to a common mistake involving positions restraints: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_ restraints_out_of_bounds If you need more specific advice, please provide us with the content of the problematic topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] cutoff-scheme in CPU GPU
Hi, all Recelly I am testing the speed of GMX4.6 on our new supercomputer. There are two parameters cutoff-scheme and nstlist . for GPUs I uesd: cutoff-scheme=Verlet nstlist = 20 I found the speed is fast. I have tested if I use cutoff-scheme=Verlet combined with nstlist=20 for CPUs, the speed was pretty fast. Could I use the same parameter for CPUs? -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] large free energy difference of mutating ATP to GTP in solution using FEP method in Gromacs-4.6.5
There are many ways for free energy calculations to go wrong. Look at http://www.alchemistry.org for some discussions. One thing I noticed (I didn't have a chance to look at everything) - you only talk about one simulation. When doing classical simulations, then you can't just mutate atoms, because classical simulations neglect quantum mechanical terms. You can only look at differences in alchemical simulations. For example, you can look at the differences between solvation free energies by performing the mutation in both water and vacuum. You have to think VERY carefully about the thermodynamic end states that you are using. On Sat, May 24, 2014 at 1:18 AM, dbaogen dbao...@gmail.com wrote: Dear all, I want to calculate the free energy difference of mutating ATP to GTP in solution using FEP method. Firstly, the hybrid topology and structure files for A (ATP) and B (GTP) state using dummy atoms were constructed. Secondly, the system is running for 10 ns to reach an equilibrium state. And then the structure at 10 ns is as the starting structure to carry out FEP calculation. In the course of FEP, the coulomb interaction was firstly changed, and then the VDW interactions. Total 32 lambda points are set in the mdp file shown in the following: integrator = sd nsteps = 10 dt = 0.002 nstenergy= 1000 nstlog = 5000 nstcalcenergy= 100 nstcomm = 1 cutoff-scheme= group rlist= 1.2 dispcorr = EnerPres vdw-type = switch ;cut-off lengths rvdw = 1.1 rvdw-switch = 1 ; Coulomb interactions coulombtype = pme rcoulomb = 1.2 fourierspacing = 0.12 ; Constraints constraints = all-bonds ; set temperature to 310K tcoupl = v-rescale tc-grps = system tau-t= 1.0 ref-t= 310 ; pressure control pcoupl = Parrinello-Rahman ref-p= 1 compressibility= 4.5e-5 tau-p= 0.5 ; and set the free energy parameters free-energy = yes sc-power = 1 sc-sigma = 0.3 sc-alpha = 0.5 sc-coul = no sc-r-power = 6 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no couple-lambda0 = vdw-q couple-lambda1 = vdw-q ; $LAMBDA$ changed from 0 to 32 init-lambda-state= $LAMBDA$ nstdhdl = 100 calc-lambda-neighbors= 1 fep-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.01 0.03 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 ;change electrostatic and then LJ interaction coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.00 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.01 0.03 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 atom part of hybrid topology file is : [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 O3 1RAGO1G 1 -0.95260 16.00 2 P 1RAG PG 21.26500 31.00 3 O3 1RAGO2G 3 -0.95260 16.00 4 O3 1RAGO3G 4 -0.95260 16.00 5 OS 1RAGO3B 5 -0.53220 16.00 6 P 1RAG PB 61.38520 31.00 7 O2 1RAGO1B 7 -0.88940 16.00 8 O2 1RAGO2B 8 -0.88940 16.00 9 OS 1RAGO3A 9 -0.56890 16.00 10 P 1RAG PA 101.25320 31.00 11 O2 1RAGO1A 11 -0.87990 16.00 12 O2 1RAGO2A 12 -0.87990 16.00 13 OS 1RAGO5* 13 -0.59870 16.00 14 CT 1RAGC5* 140.05580 12.00 15 H1 1RAGH50 150.06790 1.008000 16 H1 1RAGH51 160.06790 1.008000 17 CT 1RAGC4* 170.10650 12.00 18 H1 1RAGH40 180.11740 1.008000 19 OS 1RAGO4* 19 -0.35480 16.00 20 CT 1RAGC1* 200.03940 12.00 CT 0.01910 12.00 21 H2 1RAGH10 210.20070 1.008000 H2 0.20060 1.008000 22 N* 1RAG N9 22 -0.02510
Re: [gmx-users] binding sites with MD
Look for papers by D. E. Shaw and Gianni di Fabritiis. They have done this, but it generally takes at least microseconds or milliseconds to converge. On Sat, May 24, 2014 at 6:24 AM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns, movement of ligand molecules can be seen around certain sites only for both the runs. Can these sites be considered as binding sites? Also, ligand molecules are involved in both hydrophobic and hydrogen bonding interactions with these sites. Thanks in advance. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] binding sites with MD
Nidhi, You might be interested in this tool: http://prody.csb.pitt.edu/drugui/ Here are slide from a talk about the method: http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf And here is a tutorial: http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf I am sure that you could use GROMACS to do the simulated annealing step instead of NAMD. Tom -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] binding sites with MD
this plug-in looks interesting. However, as far as I saw from the tutorial that even we run simulation from Gromacs, this plugin can only import NAMD psf and DCD to analysis. That's a headache issue. Can you improve this vmd plugin so that it can also read Gromacs format files directly? best Albert On 05/24/2014 07:02 PM, Tom Dodson wrote: Nidhi, You might be interested in this tool:http://prody.csb.pitt.edu/drugui/ Here are slide from a talk about the method: http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf And here is a tutorial: http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf I am sure that you could use GROMACS to do the simulated annealing step instead of NAMD. Tom -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] cutoff-scheme in CPU GPU
Yes. You can. The entire program was built and was functional on CPUs well before GPUs came into the picture. Due to the way calculations are off-loaded to GPUs not all features available on CPUs are available in the GPU implementation. cutoff-scheme = Verlet is one such example. For more details please read http://www.gromacs.org/GPU_acceleration and the relevant papers. hth On Sat, May 24, 2014 at 3:52 AM, Yorquant Wang wangy...@gmail.com wrote: Hi, all Recelly I am testing the speed of GMX4.6 on our new supercomputer. There are two parameters cutoff-scheme and nstlist . for GPUs I uesd: cutoff-scheme=Verlet nstlist = 20 I found the speed is fast. I have tested if I use cutoff-scheme=Verlet combined with nstlist=20 for CPUs, the speed was pretty fast. Could I use the same parameter for CPUs? -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genion
If you want a simulation w/o Zinc as a control then build a new system/pdb w/o it (just delete the Zn line) rather than doing something exotic like turning off its charge. Turning off charges (and van der Waals parameters) is an approach more suitable for alchemical calculations http://www.alchemistry.org/wiki/Main_Page . Avoid jumping into these unless you know exactly what you are doing. On Fri, May 23, 2014 at 12:21 PM, elham tazikeh elham.tazi...@gmail.comwrote: dear users i studied on amyloid beta peptide with zinc cation and i choosed 1ze9 as my pdb file can i assume Zn without charge in protein simulation alone, or i have to using the amyloid beta peptide alone as pdb for instance,1iyt??? best wishes -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] cutoff-scheme in CPU GPU
Yes. However, a larger nstlist can be often faster with GPUs (and at high parallelization). mdrun will by default try to increase nstlist, but only if the value set in the mdp is quite low, IIRC 20. Hence, if you set nstlis=20 in the mdp, you won't get the automatic switching to 25 or 40 - settings which will often be faster. -- Szilárd On Sat, May 24, 2014 at 9:52 AM, Yorquant Wang wangy...@gmail.com wrote: Hi, all Recelly I am testing the speed of GMX4.6 on our new supercomputer. There are two parameters cutoff-scheme and nstlist . for GPUs I uesd: cutoff-scheme=Verlet nstlist = 20 I found the speed is fast. I have tested if I use cutoff-scheme=Verlet combined with nstlist=20 for CPUs, the speed was pretty fast. Could I use the same parameter for CPUs? -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] binding sites with MD
Vmd can convert trajectories, as can other tools. Google is your friend! Sent from my iPhone On May 24, 2014, at 15:13, Albert mailmd2...@gmail.com wrote: this plug-in looks interesting. However, as far as I saw from the tutorial that even we run simulation from Gromacs, this plugin can only import NAMD psf and DCD to analysis. That's a headache issue. Can you improve this vmd plugin so that it can also read Gromacs format files directly? best Albert On 05/24/2014 07:02 PM, Tom Dodson wrote: Nidhi, You might be interested in this tool:http://prody.csb.pitt.edu/drugui/ Here are slide from a talk about the method: http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf And here is a tutorial: http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf I am sure that you could use GROMACS to do the simulated annealing step instead of NAMD. Tom -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to create a new lipid molecule topology if I have .pdb file for a molecule?
Hi, I am relatively new user of Gromacs and I struggle for last few weeks to create a topology file for a new lipid molecule. I would appreciate any help on this matter. In more detail, how one creates a topology file for Charmm36, slipid, GAFF and Berger force field just knowing .pdb file for that molecule, and is there any useful tutorial or paper that discuss this matter? Thank you, Anton -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] binding sites with MD
I know that. But none of this tool is perfect and they are always this or that problem. It would be better if this tool can natively support Gromaccs. thx Albert On 05/24/2014 11:00 PM, Michael Shirts wrote: Vmd can convert trajectories, as can other tools. Google is your friend! Sent from my iPhone -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
