[gmx-users] GPU/CPU load imbalance
I have 3x GTX 970 for 1x Intel i7-5820K with X99-E WS motherboard to remove PCIe limitations. So I have 4 threads/gpu and I face load imbalances. I am wondering if it will be a good idea to use reaction-field instead of PME in order to reduce the processor load (It would be less accurate). Let me know if you have any suggestions for proper load balancing. Thank you. -- 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] GPU/CPU load imbalance
The GPU has much less load than CPU. Could you please give me some idea how to port code to GPU? Thank you. On Tuesday, 7 July 2015 2:26 AM, Szilárd Páll wrote: What kind of load imbalance? I assume you are referring to CPU-GPU imbalance as your runs are CPU-bound. In that case the only thing that helps is either porting code to CUDA or a faster CPU. Reaction field electrostatics will help too in getting better performance in CPU-bound runs, but beware that you'll have to justify the choice of deviating form the most established way of treating electrostatics! -- Szilárd On Mon, Jul 6, 2015 at 1:32 PM, Pappu Kumar wrote: I have 3x GTX 970 for 1x Intel i7-5820K with X99-E WS motherboard to remove PCIe limitations. So I have 4 threads/gpu and I face load imbalances. I am wondering if it will be a good idea to use reaction-field instead of PME in order to reduce the processor load (It would be less accurate). Let me know if you have any suggestions for proper load balancing. Thank you. -- 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] forced conformational change by MD
I want to run MD to simulate conformational change from one protein structure to another. But I am not sure how do that in gromacs. It would be like doing morphing through MD and see what kind of changed take place around the protein. Thank you. -- 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] AVX vs AVX2
I am planning to buy an Intel Haswell-E 5820 processor which supports AVX2. I am wondering if it will have better performance than i7 4930K which supports AVX. Thank you. -- 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] GPU vs Processor load
I want to run one simulation in GTX 780Ti utilizing six threads of overclocked Haswell-E 5820. So I will be running two simulations in my computer using two 780Ti. The system size varies between 60k to 300k atoms. My question is if six threads will be good enough to keep the balance between CPU and GPU load. Or I should go for a slower GPU like GTX 780 to keep the balance. Thanks. On Wed, Aug 13, 2014 at 1:55 PM, Pappu Kumar wrote: >Thanks for your info. I am planning to buy one upcoming Haswell E-5820K to >>use with 2x GTX 780Ti if feasible. So there will be six threads/GPU. I am >>wondering if it will be good enough or I should go for 2x GTX 780. Did you >mean the other way around, the 780Ti is considerable faster than the 780? What kind of systems/simulations will you be running? If you plan to use the machine for single runs and/or relatively small sysmtes, a single 780 Ti may be better. That's because at the moment in v4.6/5.0 you need domain-decomposition to use >=2 GPUs and due to the initial domain-decomposition overhead (1 to 2 domains), the scaling from one to two GPUs is OK, but not great (and typically the smaller the simulation system the worse). We are working on making it possible to use multiple GPUs within a node without domain-decomposition for the next version. >I have >plans to overclock the CPUs by 10-20%. That should work quite well. -- Szilárd >>On Tuesday, 12 August 2014 9:11 PM, Szilárd Páll >wrote: >>>Yes, it definitely will. The difference will be quite pronounced in >CPU-only runs, but if you use a GPU this will shrink and could become >relatively small depending on the turbo/frequency scaling settings >you'll use. >-- >Szilárd >>>On Tue, Aug 12, 2014 at 9:37 AM, Pappu Kumar wrote: >>I am planning to buy an Intel Haswell-E 5820 processor which supports >>AVX2. I am wondering if it will have better performance than i7 4930K which >>supports AVX. Thank you. -- 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] Performance of GTX 980 and 970
I am wondering if anyone tested the performance of new GTX 980 and 970 cards and compared to 780/780Ti/Titan using the input systems given here: http://www.gromacs.org/GPU_acceleration Thank you. -- 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] Performance of GTX 980 and 970
Thank you for your info. I am planning to buy a computer with the following configuration: Intel 5820K Corsair H100i Hydro Cooling Performance MSI X99 SLI Plus Fractal Design R4 Seasonic X 1050W I am wondering if it would be a good idea to go for 3x GTX 970 instead of 2x GTX 980 since the cost is the same. Thank you. -- 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] Performance of GTX 980 and 970
I am planning to buy 2x GTX 970 for 5820K overclocked to 4.5 GHz. I have budget limitations and not able to afford workstations with 2x CPUs. Let me know if you are aware of any cheaper alternative. Also let me know if in future Gromacs could become more GPU intensive allowing more GPUs with one CPU. Thank you. On Tuesday, 30 September 2014 5:18 PM, Szilárd Páll wrote: The 6-core Intel CPUs have only 28 PCI-E lanes rather than 40 like the 5830K/5860X which means that with a second GPU you'll get x16/x8 and with three GPUs x8/x8/x8. Also note that for the current GROMACS implementation, pairing a 5820K with two 980s will likely give a rather imbalanced hardware setup - with three 970s even more so (at least for common types of run setups). Depending on the exact use case, you may be able to make good use of 2-3 GPUs even with just a 5820K (e.g. in multi runs, one per GPU) or setups with long cut-off (or without PME), but otherwise you may not see much benefit from a second GPU, let alone a third. -- Szilárd On Mon, Sep 29, 2014 at 5:01 PM, Pappu Kumar wrote: > Thank you for your info. I am planning to buy a computer with the following > configuration: > > Intel 5820K > Corsair H100i Hydro Cooling Performance > MSI X99 SLI Plus > Fractal Design R4 > Seasonic X 1050W > > I am wondering if it would be a good idea to go for 3x GTX 970 instead of 2x > GTX 980 since the cost is the same. Thank you. > -- > 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] load imbalance: putting more load on GPU than CPU
I have 4 cpu threads available for one GTX970 card. This causes load imbalance i.e. the GPU has less load than CPU. I am wondering if it will be possible to put more load on the GPU. Thank you. -- 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] Effect of a single mutation in a protein
I did 50 ns MD simulation of WT and mutant protein in gromacs with Amber ff99sb. The mutation alters the function of the protein. The RMSD and RMSF differences in WT and mutant are <1 A. I also calculated the change in entropy of the water molecules around 4 A by Schilter's formula which seems to change in case of the mutation. Let me know how to calculate the H-bonding lifetime of the water during the simulation. Further I plotted the PC1 of C-alpha atoms of WT with the PC1 of the mutant. I am wondering if it makes sense to compare PC1 from different trajectories. Please suggest me some possible analysis. Thank you. -- 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] Effect of a single mutation in a protein
I have already used g_hbond. I am not sure how accurate is the H-bond lifetime
calculation. Also the trajectory snapshots need to be saved quite often. Could
you tell me how to interpret output from g_hbond -ac :
@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"
Could you tell me how to project the configurations of the mutant simulation
on WT PC1? Are you aware of any paper where I can read more about it? Can I
compare the PC1 vs PC2 in case of WT and mutant?
I am trying to find out how such mutation buried inside the protein away from
the ligand binding pocket can influence the function of the protein. I actually
see some changes in the positon of the bound ATP in the mutant compared to the
WT. But I am not sure how reliable it is due to the inaccuracies in
parameterization.
I also calculated the Gibbs free energy landscape by g_sham using Rg and RMSD.
The value varies from 0-6.5 kJ/mol in both cases but the regions with ~0 kJ/mol
has changed.
Thank you.
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[gmx-users] Checking the possibility of one complex out of possible two
I got two long protein complexes made out of 20 monomers of ~300 residues. But only one complex exists biologically. I am trying to find out the energetically favourable complex by MD simulation in gromacs 4.6.5. Initially I took out a dimer from the complexes and ran steepest descent followed by L-BFGS minimization . Although the total energy was lower in one dimer, after the L-BFGS, the energy was similar. Then I ran 50ns MD simulation and calculated the interaction energies between the monomers which is similar in both cases. The idea was that in the wrong confomation the interaction energy would be lower. Now I am wondering how to find out the correct conformation between the two possibilites. I also checked the free energy of solvation which is different in both cases. I am not sure if it is a clear indicator of stability since entropy is not taken into account. Let me know if you have any ideas. I am planning to run coarse grained simulations in MARTINI. Thank you. -- 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] Effect of a single mutation in a protein
Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
atoms of one trajectory and then projected the other trajectory on it.
I obtained the ATP parameters from a paper. Like all simulations, MD has some
limitations. So I don't want to highlight the things which may not be correct.
There is no unfolding. Also the gibbs energy surface projected on PC1 and PC2
looks quite different than RMSD vs. Rg surface calculated by g_sham (also the
lowest energy structures.)
Can I calculate del del G by TI? I am not sure how to define the reaction
coordinates. Is it a good idea to do umbrella sampling between two states to
determine the free energy?
On Thursday, 27 March 2014 8:35 AM, Justin Lemkul wrote:
On 3/26/14, 2:24 PM, Pappu Kumar wrote:
> I have already used g_hbond. I am not sure how accurate is the H-bond
> lifetime calculation. Also the trajectory snapshots need to be saved quite
> often. Could you tell me how to interpret output from g_hbond -ac :
>
There should be references provided in the g_hbond output when calculating
lifetimes. At the very least, they're in the manual. So you can determine for
yourself how reliable the outcome is.
> @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
> @ s1 legend "Ac(t)"
> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
> @ s3 legend "-dAc\sfs\v{}\z{}/dt"
>
Plotting these data sets in XmGrace will clear things up.
> Could you tell me how to project the configurations of the mutant simulation
> on WT PC1? Are you aware of any paper where I can read more about it? Can I
> compare the PC1 vs PC2 in case of WT and mutant?
>
See g_anaeig -h, as well as previous discussions in the list archive on doing
this.
>
> I am trying to find out how such mutation buried inside the protein away from
> the ligand binding pocket can influence the function of the protein. I
> actually see some changes in the positon of the bound ATP in the mutant
> compared to the WT. But I am not sure how reliable it is due to the
> inaccuracies in parameterization.
>
Well, if your parametrization is inaccurate and you know it is, what use are
the
simulations? Or are you just wondering if there is a possibility of
inaccuracies? Either way, that's something that should be sorted out long
before doing any real simulations :)
>
> I also calculated the Gibbs free energy landscape by g_sham using Rg and
> RMSD. The value varies from 0-6.5 kJ/mol in both cases but the regions with
> ~0 kJ/mol has changed.
>
Do the proteins unfold? If not, I doubt Rg vs. RMSD is a very sensitive metric
of anything. You can, of course, map back the locations of the energy minima
to
see if there are any interesting differences there, but such a plot (Rg vs.
RMSD) is probably only useful in protein (un)folding simulations.
-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
==
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[gmx-users] simulation of a trimer
I got a protein which undergoes conformational change during trimer formation. There is a cryoEM structure of the trimer. So I took the trimer structure and replaced one monomer with a monomer without conformational change. Then I ran a 50 ns MD md simulation with Amber99sb FF in gromacs 4.6.5, restraining two other monomers expecting to see the conformational change in the other trimer. But there was no change in the monomer structure. Subsequently, I made all the monomers flexible and ran 50 ns MD. Now I can see the change in monomer structure. But it has become difficult to completely align the final structure from MD with the cryoEM structure. So I am wondering what so of analysis to do in order to show that the expected conformational change is taking place. For example calculating the angle between the center of masses of the monomers, PCA, mutual information etc. I was also thinking about using MARTINI to restrain two monomers by elastic network and then perturb the other one monomer to observe changes in the system. Thank you. -- 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] Checking the possibility of one complex out of possible two
In the two protein dimers, the location of one monomer is at the opposite side of the other monomer : (| 0 and 0 |) when they are aligned (0 - common monomer, (| or |) the other monomer). So it would be hard to get the reaction coordinate for PMF calculation. I am wondering if I can compare the free energy of decoupling from water of two dimers separately by TI (g_bar). Can I use the same techinique in case of a point mutation? Thank you. On Friday, 28 March 2014 7:40 AM, Justin Lemkul wrote: On 3/27/14, 1:59 PM, Pappu Kumar wrote: > I got two long protein complexes made out of 20 monomers of ~300 residues. > But only one complex exists biologically. I am trying to find out the > energetically favourable complex by MD simulation in gromacs 4.6.5. Initially > I took out a dimer from the complexes and ran steepest descent followed by > L-BFGS minimization . Although the total energy was lower in one dimer, after > the L-BFGS, the energy was similar. > > Then I ran 50ns MD simulation and calculated the interaction energies between > the monomers which is similar in both cases. The idea was that in the wrong > confomation the interaction energy would be lower. > > Now I am wondering how to find out the correct conformation between the two > possibilites. I also checked the free energy of solvation which is different > in both cases. I am not sure if it is a clear indicator of stability since > entropy is not taken into account. Let me know if you have any ideas. I am > planning to run coarse grained simulations in MARTINI. Thank you. > Calculating an actual deltaG of binding (i.e. a PMF) between the two monomers is about the only legitimate way I can think of to do this. The values of potential energy in a minimized structure are totally dependent on the force field, as are the nonbonded interaction energies, which (more importantly) aren't necessarily parametrized to be anything useful. -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] Checking the possibility of one complex out of possible two
Decoupling seems only feasible for small ligands. I tried to decople a protein but the grompp does not converge. Could you tell me the maximum size of the molecule that is feasible for decoupling? I already calculated the free energy of solvation by APBS. Now I am pulling out one monomer from the other in both cases and checking the PMF along the trajectory using your tutorial on umbrella sampling. Thanks. On Monday, 31 March 2014 8:06 PM, Justin Lemkul wrote: On 3/31/14, 6:07 AM, Pappu Kumar wrote: > In the two protein dimers, the location of one monomer is at the opposite side > of the other monomer : > > (| 0 and 0 |) > > when they are aligned (0 - common monomer, (| or |) the other monomer). So it > would be hard to get the reaction coordinate for PMF calculation. > > I am wondering if I can compare the free energy of decoupling from water of > two > dimers separately by TI (g_bar). Can I use the same techinique in case of a > point mutation? Thank you. > Doubtful. Decoupling a whole protein is impractical from both a performance and analysis standpoint. The simulations will probably never reach convergence and will sample a bunch of really unphysical states. Something like MM/PBSA would be much more sensible. -Justin > On Friday, 28 March 2014 7:40 AM, Justin Lemkul wrote: > > > On 3/27/14, 1:59 PM, Pappu Kumar wrote: > > I got two long protein complexes made out of 20 monomers of ~300 residues. > > But only one complex exists biologically. I am trying to find out the > > energetically favourable complex by MD simulation in gromacs 4.6.5. >Initially > > I took out a dimer from the complexes and ran steepest descent followed by > > L-BFGS minimization . Although the total energy was lower in one dimer, >after > > the L-BFGS, the energy was similar. > > > > Then I ran 50ns MD simulation and calculated the interaction energies >between > > the monomers which is similar in both cases. The idea was that in the wrong > > confomation the interaction energy would be lower. > > > > Now I am wondering how to find out the correct conformation between the two > > possibilites. I also checked the free energy of solvation which is >different > > in both cases. I am not sure if it is a clear indicator of stability since > > entropy is not taken into account. Let me know if you have any ideas. I am > > planning to run coarse grained simulations in MARTINI. Thank you. > > > > > Calculating an actual deltaG of binding (i.e. a PMF) between the two monomers > is > about the only legitimate way I can think of to do this. The values of > potential energy in a minimized structure are totally dependent on the force > field, as are the nonbonded interaction energies, which (more importantly) > aren't necessarily parametrized to be anything useful. > > -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 <mailto:jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > > == > > -- == 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.
[gmx-users] All-atom MD simulation of a protein at 323K and 283K
I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation in gromacs with Amber99sb in these temperature since force field parameterization was carried out in room temperature. I am also thinking about running simulated annealing from 323K to 283K in order to compare the stability of the two proteins. Thank you. -- 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] Indicators of protein stability
I am trying to find out why a protein from a thermophilic organism is more stable compared to the non-thermophilic organism although the sequence similarity is very high. So I conducted MD simulations in low and high temperatures. I am wondering which statistic would be good to define the stability (i.e. if there is any existing paper) apart from RMSD, RMSF, Rg and secondary structure. Thank you. -- 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.
