[gmx-users] Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

Thank you for the advice Dr. Warren, I often find the same problem with charges and parameters, and have pulled some from the web in some instances. I have an old CRC book with tables when in doubt, But I wounder if anyone is interested in just making a tabulation, or wiki site to deposite t

Re: [gmx-users] Re: distance/direction PMF

Hi Justin I think what is happening is that grompp is returning the projection of the current vector between the two reference groups onto the stated vector in the mdp file. i.e the dot product of the two vectors. The resulting PMF plot must therefore be a function of this varying cross product.

Re: [gmx-users] oplsaa vs. charmm

Thank you all for your comments! Let me give you more details about my case: I want to study the interaction modes of known inhibitors with the monomeric state of an IDP (~100 aa). IDPs only assume secondary structure when in complex with their partners, hence there are no crystal structures of th

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the published values seem to be inc

Re: [gmx-users] oplsaa vs. charmm

hello My feeling is that you can probably get meaningfull result by using implicit water model plus some experimental constrain. If you have a well defined reaction coordinate, umbrella sampling will help. As you planed, you can also simulate unfolding process and just invert it to get the folding

[gmx-users] All-atom topologies for lipid head groups

Dear Gromacs users, I am a new user and I am trying to study the physical properties of the interactions between cytosolic proteins and lipids. I have created the Berger-Gromos combination, as described by Mr. Justin Lemkul in his KALP15 in DPPC tutorial, as well as Berger-OplsAA, as descri

Re: [gmx-users] Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

lloyd riggs wrote: Thank you for the advice Dr. Warren, I often find the same problem with charges and parameters, and have pulled some from the web in some instances. I have an old CRC book with tables when in doubt, But I wounder if anyone is interested in just making a tabulation, or wiki

[gmx-users] Re: oplsaa vs. charmm (Thomas Evangelidis)

Hi, You may want to look at the papers below, which deal with a similar problem. Also, I would run multiple simulations for each case. Ran. @Article{ScherzerAttali:2010:PLoS-One:20559435, author = "Scherzer-Attali, R and Pellarin, R and Convertino, M and Frydman-Marom, A and Egoz-Matia, N and P

Re: [gmx-users] All-atom topologies for lipid head groups

Ioannis Beis wrote: Dear Gromacs users, I am a new user and I am trying to study the physical properties of the interactions between cytosolic proteins and lipids. I have created the Berger-Gromos combination, as described by Mr. Justin Lemkul in his KALP15 in DPPC tutorial, as well as Berg

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Thomas Piggot wrote: Hi Igor, Thanks for the reply but I think you slightly missed the point I was trying to make. I followed the approach you mention for the double bond and (with the two force fields I tried) got the values I discussed in my last email, which when compared to the publishe

Re: [gmx-users] Why does the -append option exist?

Hi, On Thu, Jun 9, 2011 at 2:55 AM, Roland Schulz wrote: > Hi, > > yes that helps a lot. One more question. What filesystem on hopper 2 are > you using for this test (home, scratch or proj, to see if it is Lustre or > GPFS) ? > I used home. > And are you running the test on the login node or

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical results to those in my previous message. The other thing is that the r

Re: [gmx-users] All-atom topologies for lipid head groups

Hi, A force file like this does exist (http://pubs.acs.org/doi/abs/10.1021/jp800687p) but be aware, like the CHARMM27 force field it is based upon, you will need to use surface-tension to keep these lipids in the correct phase. Cheers Tom Justin A. Lemkul wrote: Ioannis Beis wrote: Dear

[gmx-users] creating topology using g_x2top

Dear all , I want to simulate a double walled nano tube in spc water i had made the pdb file now if i use g_x2top for creating the topology file it gives me the following error . Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa* it gives the following error *Can not find forcef

Re: [gmx-users] creating topology using g_x2top

sreelakshmi ramesh wrote: Dear all , I want to simulate a double walled nano tube in spc water i had made the pdb file now if i use g_x2top for creating the topology file it gives me the following error . Now if i run * g_x2top -f out.pdb -o out.top -ff oplsaa* it gives the foll

[gmx-users] RE: Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

I also found this usefull, but have a question on what one would consider the standard. from eyeballing mostly the charges I get for .itp files from PRODRG server fall into mullikin charges, but usually 3-4 dont or have no charge, but I woundered if the ESP or AIM charges would be beter. From

Re: [gmx-users] RE: Re:Umbrella sampling of phosphate ion binding (Dallas Warren)

lloyd riggs wrote: I also found this usefull, but have a question on what one would consider the standard. from eyeballing mostly the charges I get for .itp files from PRODRG server fall into mullikin charges, but usually 3-4 dont or have no charge, but I woundered if the ESP or AIM charges wo

[gmx-users] Re: problem in g_density

Hi Mark, The set of frames is arbitrary, overall I do not expect any sudden significant change in density. I calculated the density profiles by coinciding end of intervals, i.e instead of 5-10, 10-15, 15-20 and 5-20 ns, I calculated 4999-1, -15000, 14999-end and 4999 - end ps. (simul

Re: [gmx-users] Essential dynamics - concepts

Dear Sir, Thank you Sir for the clarification. Need to explore about this. Thanking you With Regards M. Kavyashree On Wed, Jun 8, 2011 at 2:35 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > > Thanks sir. I will go through them. However I have referred - > > "A Tutorial on Principle component

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Further to my last message we have managed to use a tcl script in VMD to calculate the order parameters for the POPC chains in the CHARMM36 simulation. I have put the values for this calculation and the values I obtained using g_order (over the same period in the same trajectory) below (this is

[gmx-users] Comparing single with double precision runs

Dear Gromacs-users, I compiled a single and a double precision version of gromacs 4.5.4 (MPI enabled). The differences between single and double precision runs have been discussed in older threads (2005/2008) in this mailing list before. At least, I did not understand completely, which parts or

Re: [gmx-users] Comparing single with double precision runs

On Thu, 09 Jun 2011 17:30:10 +0200 kalav...@gmx.net wrote: > Dear Gromacs-users, > > I compiled a single and a double precision version of gromacs 4.5.4 > (MPI enabled). The differences between single and double precision > runs have been discussed in older threads (2005/2008) in this mailing > li

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Dear Thomas: I agree with your conclusions about g_order. My usage of the Berger POPC lipids in combination with the g_order command (as per the instructions in http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields order parameters of 0.193 and 0.051 for the first and sec

[gmx-users] local pressure calcuation for Gromacs-4.5

Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Amit Choubey wrote: Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? I don't know what the development statu

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Dear all, >> >> I saw an unanswered post at >> http://lists.gromacs.org/piperma

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Amit Choubey wrote: Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? Run the bootstrap script. It generates the configure script. -Justin On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

chris.ne...@utoronto.ca wrote: Dear Thomas: I agree with your conclusions about g_order. My usage of the Berger POPC lipids in combination with the g_order command (as per the instructions in http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields order parameters of 0.193

[gmx-users] 1,4 hydrogen pairtypes in CHARMM36

This is more a question for Tom or Pars: I noticed that in charmm36.ff/ffnonbonded.itp there are no hydrogen-hydrogen pairtypes even though the rtp databases specify HH14 = 1 Is this because when using default nrexcl = 3, 1,4 gets excluded? So should I even bother converting revised-CGenFF atomt

[gmx-users] Invalid angle type 0 error during minimization.

Dear all, i am trying to simulate a double walled cnt in tip4p water using oplsaa force field. first i used *g_x2top -f carbon.pdb -o carbon.top* ( successfully created the topology) * editconf -f carbon.pdb -o carbon_newbox.gro -c -box 3.41840 3.44350 5.5965 genbox

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Ting Zhou requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Ting Accept invitation from Ting Zhou http://www.linkedin.com/e/-85v1n9-goqo1i6f-x/Xl9gj

[gmx-users] Atoms in the .top are not numbered consecutively from 1

Dear all, when i run energy minimization i get the following error. the topology file was created from the starting pdb file using g_x2top *grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3* Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 348,