[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pulling along hexane-water interface
Sorry forgot to write the subject in previous mail. Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position restrained one hexane molecule in the bulk of hexane (pull_group0) and trying to pull the polypeptide (pull_group1) towards it. But though the polypeptide is getting pulled, the hexane layer is breaking in the process. The pulling options used are as follows, pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = 3 pull_group1 = Protein pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 We have also played a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position restrained one hexane molecule in the bulk of hexane (pull_group0) and trying to pull the polypeptide (pull_group1) towards it. But though the polypeptide is getting pulled, the hexane layer is breaking in the process. The pulling options used are as follows, pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = 3 pull_group1 = Protein pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 We have also played a bit with the pull rate and pull constant, but same thing happens. Are we doing something wrong? Can you please help? -- Prithvi Raj Pandey National Chemical Laboratory, Pune 411008. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water mediated hydrogen bond
Hi all, I would like to measure the water mediated hydrogen bond between the ligand and the protein. When I searched the forum I could able to get the link (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) for the script with which we can get the above mentioned objective. But I'm not sure how to use it Can any one help me with what data I should have before running the script and how I can get such a data and also how shuld I use the data as a input for the script?. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/water-mediated-hydrogen-bond-tp5003358.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: hydrophobic contacts
Hi all thanks for your valuable suggestions. But still i'm not clear. I have tried using the .tpr file with make_ndx but the index group is displayed is similar to that of the one with .gro file. I have manually identified the residues and when i ran the g_mindist with the ligand 0f 18 atoms against the residues of 174 atoms i'm getting contacts ranging from 87 to 40. please help me with stepwise instruction as I cant follow the thing. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5003043.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: hydrophobic contacts
Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5002931.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_mindist - reg
Hi, can you suggest me how can i identify or specify the hydrophobic atoms to the index files. -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756p5002819.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: g_mindist - reg
thank you justin ... I have given the entire protein as one group.. now will it be ok or i need to give only hydrophobic resides alone as a index group. Thank you once again for yor response -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756p5000771.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_mindist - reg
hi all, I would like to measure the hydrophobic interaction of the ligand against the protein during the simulation . From the forum I learnt g_mindist will be the better tool. But when i used the command g_mindist -f traj.xtc -s topol.tpr -n index.ndx -on numcont.xvg -group and selected protein as group1 and ligand as group 2 i get the result like this g_mindist -f traj.xtc -s pull.tpr -n index.ndx -on numcont.xvg -group # # g_mindist is part of G R O M A C S: # # Good ROcking Metal Altar for Chronical Sinners # @title "Number of Contacts < 0.6 nm" @xaxis label "Time (ps)" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Protein-UNK" 0.00e+0021 1.00e+0021 2.00e+0021 3.00e+0021 4.00e+0021 5.00e+0021 6.00e+0021 7.00e+0021 8.00e+0021 9.00e+0021 1.00e+0121 1.10e+0121 1.20e+0121 1.30e+0121 1.40e+0121 1.50e+0121 1.60e+0121 1.70e+0121 1.80e+0121 1.90e+0121 2.00e+0121 2.10e+0121 2.20e+0121 2.30e+0121 2.40e+0121 2.50e+0121 2.60e+0121 2.70e+0121 2.80e+0121 2.90e+0121 3.00e+0121 3.10e+0121 3.20e+0121 3.30e+0121 3.40e+0121 3.50e+0121 3.60e+0121 3.70e+0121 3.80e+0121 3.90e+0121 4.00e+0121 4.10e+0121 4.20e+0121 4.30e+0121 4.40e+0121 4.50e+0121 4.60e+0121 4.70e+0121 4.80e+0121 4.90e+0121 5.00e+0121 5.10e+0121 5.20e+0121 5.30e+0121 I would like to know what ever the data I've obtained is the number of hydrophobic interaction between the ligand and protein or I am wrong somewhere. Please help me. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/g-mindist-reg-tp5000756.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] write velocity and coordinates with template.c
> Message: 2
> Date: Thu, 26 Jul 2012 20:56:00 +1000
> From: Mark Abraham
> Subject: Re: [gmx-users] Writing velocity of particles using
> template.c
> To: Discussion list for GROMACS users
> Message-ID: <50112240.5000...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 26/07/2012 8:22 PM, prithvi raj pandey wrote:
>> Dear gmx users,
>>
>> I am using template.c of gromacs 4.0.7 for writing my own analysis
>> tool. When I am using the fr.x[i][XX], it writes the coordinates of
>> the particles (i crosschecked it with the coordinates written by the
>> trjconv command). But the problem arises when I use fr.v[i][XX] for
>> writing the velocities of the particles or fr.f[i][XX] for writing the
>> force. The program compiles fine by using make command. But finally
>> the template stops showing segmentation fault. The main loop is as
>> follows -
>>
>> do {
>>
>> fprintf(fp,"BOX %f %f %f %f
>> \n",fr.time,fr.box[XX][XX],fr.box[YY][YY],fr.box[ZZ][ZZ]);
>>
>> for (i=0; i> {
>> fprintf(fp,"Velocity at t=%8.3f : %f %f
>> %f\n",fr.time,fr.v[i][XX],fr.v[i][YY],fr.v[i][ZZ]);
>> }
>>} while(read_next_frame(status,&fr));
>>
>> Am I using the variable used for writing velocity/force wrongly?
>
> Did you verify that the trajectory has velocities, and that you read
> them, and that they're found in fr.v? Look at the code for a tool that
> reads velocities (g_velacc, I guess).
>
> Mark
>
>
Dear Mark,
I ran the g_velacc command, it works fine and writes the output .xvg
file. Also i generated a .gro containing both positions and velocity
using the trjconv command.
By this time I could wirte the velocity using template.c by changing
TRX_READ_X toTRX_READ_V and by adding *vtop in rvec in the following
section of template.c
t_topology top;
intePBC;
char title[STRLEN];
t_trxframe fr;
rvec *xtop,*vtop;
matrix box;
intstatus;
intflags = TRX_READ_V;
But the problem now is it only writes velocity using the variable
fr.v[i][XX], but the coordinates are not being written by the variable
fr.x[i][XX]. I intend to use both coordinates and velocity for my
program.
It seems to that the "flags =" can only take one value. This is
because I tried to write both TRX_READ_X and TRX_READ_V under the same
flags variable, but it did not compile.
Am I doing something seriously wrong?
Prithvi Raj
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Writing velocity of particles using template.c
Dear gmx users,
I am using template.c of gromacs 4.0.7 for writing my own analysis
tool. When I am using the fr.x[i][XX], it writes the coordinates of
the particles (i crosschecked it with the coordinates written by the
trjconv command). But the problem arises when I use fr.v[i][XX] for
writing the velocities of the particles or fr.f[i][XX] for writing the
force. The program compiles fine by using make command. But finally
the template stops showing segmentation fault. The main loop is as
follows -
do {
fprintf(fp,"BOX %f %f %f %f
\n",fr.time,fr.box[XX][XX],fr.box[YY][YY],fr.box[ZZ][ZZ]);
for (i=0; ihttp://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints in SMD
Hi all, It may be naive but I would like to get some clear explanation in SMD ( COM pulling) reg. The question is, Before performing the COM-pulling (incase of protein ligand complex) do we need to position restrain the ligand using genrestr and then add the topology to the topol.top file. If not why should not we restrain the ligand. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/position-restraints-in-SMD-tp4999444.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water bridge
Hi all, I have an protein and drg complex. I've done the MD in SPC water environment. Now I would like to check number of hydrogen bond formed between the drug and protein, water as well. What will the right command for me to analyse. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/water-bridge-tp4999370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: specifying the direction of Pull in US
Thanks for ur suggestion Justin, I'm facing trouble in setting that vector, actually I cant figure out how can i set up a vector. Is there any easier way with which i can set up a vector. Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140p4999177.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: specifying the direction of Pull in US
hi , When i applied distance I cant have control over the direction of the pull. The ligand is not exactly pulled along the direction i meant to pull -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140p4999155.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] specifying the direction of Pull in US
Hi all, I am working on steered molecular dynamics and In that I would like to pull the ligand ( already in complex with protein) away from the reference amino acid ( which I've selected so that I can direct the ligand to get closure to my desired amino acid residue). Now the thing is when I used VMD to assign the direction, The desired direction of mine is not along the proper x, y, or in Z axis. So my question is how can i specify the direction in a situation like this. I've seen in other discussions people have used pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/specifying-the-direction-of-Pull-in-US-tp4999140.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: chi1/chi2
Dear Mark, Thanks for your reply.. can you suggest me how i can take the plot with 0 to 360 angle. I've tried periodic of g_chi with -all option to generate the chi1/chi2 plot for the each and every amino acid residue but i couldnt do it properly can you suggest on this. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/chi1-chi2-tp4998884p4998998.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: COM Pulling
Dear Justin, I've tried what you have suggested. I have used the pull code and gave 4 amino acid residues as a reference group. The location of the groups are one below the ligand (in the protein core) and 3 were on the above ( towards the active site gorge). When i used the code pull = umbrella pull_geometry = distance ; simple distance increase pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = DRG pull_group1 = reference groups pull_rate1 = 0.003 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 the ligand migrated more and more towards the protein , not coming out of the protein through the channel i defined by referring the amino acid groups when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can not be zero. when i was trying to use pull_geometry = direction the system blowed up. but the pull_geometry = distance worked well. please give me a suggestion to resolve the issue -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998989.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: COM Pulling
Thanks for your reply Justin. >From your umbrella tutorial I thought the reference group should be the protein. Now from your reply i think I can specify any amino acid residue in the protein and I can drive the ligand towards the residue. where I need to specify the group If i'm using the pull code ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = DRG pull_group1 = ?? pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 how can i specify the residue if i want to pull towards the direction of 3 amino acids, and I've included in the index file please help... -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944p4998955.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] COM Pulling
HI , I have been performing SMD after reading bevan lab tutorial. The tutorial was very informative in basic aspects. Now I have my ligand inside the protein and I wan to pull it out in a specific direction. I applied force separately along the X, Y and Z axis . In which none of the pull seems to be proper. In the sense the ligand didn't come through the already predicted channel. So my question is can i specify the direction of the pull by mentioning the amino acid residues lined along the channel of the protein ? if i can what is the modification I should do to achieve the objection. Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/COM-Pulling-tp4998944.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] chi1/chi2
during the simulation. I tried g_chi to obtain chi1 and chi2 values at the end I'm getting the plot withe values ranges from -180 to 180 . But in papers people have reported in 360 degree how can i get the data. Please give me suggestions -- View this message in context: http://gromacs.5086.n6.nabble.com/chi1-chi2-tp4998884.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in atom type
Dear users,
Force field: 53a6
water model: spcTermini : NH3+ and COO-
After the command:pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top
-ter -merge -ignh
I have the following error:
Fatal error:
Fatal error:
Atom LPG1 in residue CYS 143 was not found in rtp entry CYSH with 8 atoms
while sorting atoms.
What is the appropriate atom type corresponding to LPG1 and LPG2 for cysteine?
Thanx
Anu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] atomic concentration in x and y axis
Hello, I have done simulations on cyclic peptide nanotubes and trying to calculate the atomic concentration in the x and y axis, to measure the diameter of the tube. I have tried using the g_rdf, but the results are confusing to interpret. Here is the steps which I followed, 1. using trjconv, rotational and translational motions are removed from the centered trajectory. 2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg (I understood that the "-rdf atom" option is the default one and this will calculate the atomic distribution in the x and y plane) I am not sure whether the elimination of translational and rotational motions is enough to calculate this property, should I have to align the structure in the z axis using the PCA analysis? Regards, Raj. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] concentration distribution
Hello, I would like to calculate the concentration distribution of atoms along the x and y axis from the trajectory. Can anybody suggest me a tool to calculate this? regards, Raj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] solvation box type for nanotubes
Hello, Can we use rhombic dodecahedron solvation box for the PMF calculation on the small molecule diffusion into carbon nanotube. so that we can reduce 29% calculation time. If so then what could be the box size? Thank you. Regards, raj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Intermolecular RDF in DPPC
Dear gmx users, I want to calculate intermolecular RDF between N and carbonyl oxygen atoms in a DPPC bilayer. As suggested in some mails in the mailing list i wanted to generate one tpr file for the purpose containing exclusion 49 (as united atom model of DPPC contains 50 atoms). But while generating the tpr file using the following command grompp -f grompp.mdp -p topol.top -c dppc08.pdb -o rdf.tpr the grompp program hangs saying checking input for internal consistency... processing topology... Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6nb.itp Opening library file /export/softexport/gromacs/share/gromacs/top/ffG53a6bon.itp Opening library file /export/softexport/gromacs/share/gromacs/top/ff_dum.itp Generated 165 of the 1596 non-bonded parameter combinations Opening library file /export/softexport/gromacs/share/gromacs/top/spc.itp Excluding 49 bonded neighbours molecule type 'DPPC' and does not proceed further. What is wrong? Can anyone please help? -- Prithvi Raj Pandey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with g_density
Dear gmx-users, I have generated 40ns trajectories for DPPC bilayer - water system. The whole 40ns was generated in small trajectories and finally I concatenated all the small trajectories to a big 40 ns trajectory using the following options in trjcat trjcat -f -o -settime -tu Now the problem is when I am trying to plot partial density along the bilayer - water interface axis (i.e. Z) using the big trajectory for different groups (e.g., water,DPPC etc.), density for water comes around 150 kg/m^3. But for any of the small trajectories the value is ok (i.e. around 1000). The plots were done using the folloing tool g_density -f-o -n -s -d Z Can anyone help? -- Prithvi Raj Pandey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
